NP-MRD: Showing NP-Card for cladribine (NP0213507)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-05 12:31:09 UTC

Updated at

2022-09-05 12:31:09 UTC

NP-MRD ID

NP0213507

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cladribine

Description

Cladribine, also known as 2-cda or 2CLADO, belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2. 2'-Deoxyadenosine in which the hydrogen at position 2 on the purine ring has been substituted by chlorine. Cladribine is a drug which is used for the treatment of active hairy cell leukemia (leukemic reticuloendotheliosis) as defined by clinically significant anemia, neutropenia, thrombocytopenia, or disease-related symptoms. Also used as an alternative agent for the treatment of chronic lymphocytic leukemia (cll), low-grade non-hodgkin's lymphoma, and cutaneous t-cell lymphoma. Cladribine is a moderately basic compound (based on its pKa). cladribine was first documented in 2007 (PMID: 17852710). Cladribine is a potentially toxic compound (PMID: 19463072) (PMID: 19576186).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
   -5.0821    0.6424    0.9802 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9763    0.4563    0.1101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0474    0.7447   -1.2122 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9951    0.5665   -2.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2350    0.9837   -3.7250 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.8149    0.0892   -1.5750 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6804   -0.2122   -0.2912 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7606   -0.0314    0.5642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3396   -0.4094    1.7641 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0693   -0.8089    1.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442   -0.6927    0.4195 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6807   -1.0395   -0.0065 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1531   -0.1930   -1.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6684   -0.3327   -0.9707 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0797   -1.5942   -1.4549 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7515   -0.3800    0.5240 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0474    1.0130    1.0897 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2475    1.4636    0.5827 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5621   -0.8375    1.0205 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3995   -0.1737    1.5423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5758    1.5382    1.0767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4899   -1.1690    2.5431 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7503   -2.0968   -0.3403 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9179    0.8731   -1.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8913   -0.6139   -2.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2205    0.4842   -1.4360 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0283   -2.2824   -0.7266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948   -1.0273    0.8805 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1213    0.9454    2.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1980    1.6749    0.7985 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1974    2.4197    0.3776 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
 11  7  1  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
  7  8  1  0
 19 12  1  0
  1 20  1  0
  1 21  1  0
 10 22  1  0
 12 23  1  6
 13 24  1  0
 13 25  1  0
 14 26  1  6
 15 27  1  0
 16 28  1  6
 17 29  1  0
 17 30  1  0
 18 31  1  0
M  END

242
  Mrv0541 02231214322D          

 19 21  0  0  1  0            999 V2000
    1.6500   -0.5556    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.3467    0.7358    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2852    1.6299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1323    2.7996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -0.7167    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5741   -2.0446    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.5556    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.7931    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -3.0306    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8305    0.0675    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6170    1.1461    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6155    0.3211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8328    1.4024    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5792    2.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.9681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0556   -1.3806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -1.7931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -2.2056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.9681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 19  1  0  0  0  0
  2 10  1  0  0  0  0
  2 13  1  0  0  0  0
 11  3  1  1  0  0  0
  4 14  1  0  0  0  0
 10  5  1  6  0  0  0
  5 15  1  0  0  0  0
  5 16  1  0  0  0  0
  6 16  2  0  0  0  0
  6 17  1  0  0  0  0
  7 15  2  0  0  0  0
  7 19  1  0  0  0  0
  8 18  1  0  0  0  0
  8 19  2  0  0  0  0
  9 18  1  0  0  0  0
 10 12  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0213507

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C2=NC(Cl)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H12ClN5O3/c11-10-14-8(12)7-9(15-10)16(3-13-7)6-1-4(18)5(2-17)19-6/h3-6,17-18H,1-2H2,(H2,12,14,15)/t4-,5+,6+/m0/s1

> <INCHI_KEY>
PTOAARAWEBMLNO-KVQBGUIXSA-N

> <FORMULA>
C10H12ClN5O3

> <MOLECULAR_WEIGHT>
285.687

> <EXACT_MASS>
285.062866982

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
25.933311613576564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol

> <ALOGPS_LOGP>
-0.12

> <JCHEM_LOGP>
-0.2817754633333334

> <ALOGPS_LOGS>
-1.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.784914754981045

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.886716048865388

> <JCHEM_PKA_STRONGEST_BASIC>
1.3268966303757452

> <JCHEM_POLAR_SURFACE_AREA>
119.30999999999999

> <JCHEM_REFRACTIVITY>
67.18350000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.35e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cladribine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 242                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Cl   UNK     0       3.080  -1.037   0.000  0.00  0.00          Cl+0
HETATM    2  O   UNK     0       8.114   1.373   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      11.732   3.042   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.580   5.226   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       8.538  -1.338   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       8.538  -3.817   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       5.748  -1.037   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       4.414  -3.347   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       5.748  -5.657   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       9.017   0.126   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.485   2.139   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.482   0.599   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.021   2.618   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.548   4.083   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.081  -1.807   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.437  -2.577   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.081  -3.347   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.748  -4.117   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.414  -1.807   0.000  0.00  0.00           C+0
CONECT    1   19                                                            
CONECT    2   10   13                                                       
CONECT    3   11                                                            
CONECT    4   14                                                            
CONECT    5   10   15   16                                                  
CONECT    6   16   17                                                       
CONECT    7   15   19                                                       
CONECT    8   18   19                                                       
CONECT    9   18                                                            
CONECT   10    2    5   12                                                  
CONECT   11    3   12   13                                                  
CONECT   12   10   11                                                       
CONECT   13    2   11   14                                                  
CONECT   14    4   13                                                       
CONECT   15    5    7   17                                                  
CONECT   16    5    6                                                       
CONECT   17    6   15   18                                                  
CONECT   18    8    9   17                                                  
CONECT   19    1    7    8                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S,5R)-5-(6-Amino-2-chloropurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol	ChEBI
2-CdA	ChEBI
2-Chloro-2'-deoxy-beta-adenosine	ChEBI
2-Chloro-6-amino-9-(2-deoxy-beta-D-erythro-pentofuranosyl)purine	ChEBI
2-Chloro-deoxyadenosine	ChEBI
2-Chlorodeoxyadenosine	ChEBI
2ClAdo	ChEBI
Cladribina	ChEBI
Cladribinum	ChEBI
CldAdo	ChEBI
Leustatin	Kegg
Mavenclad	Kegg
2-Chloro-2'-deoxy-b-adenosine	Generator
2-Chloro-2'-deoxy-β-adenosine	Generator
2-Chloro-6-amino-9-(2-deoxy-b-D-erythro-pentofuranosyl)purine	Generator
2-Chloro-6-amino-9-(2-deoxy-β-D-erythro-pentofuranosyl)purine	Generator
2-Chloro-2'-deoxyadenosine	HMDB
Chlorodeoxyadenosine	HMDB
2'-Deoxy-2-chloroadenosine	HMDB

Chemical Formula

C₁₀H₁₂ClN₅O₃

Average Mass

285.6870 Da

Monoisotopic Mass

285.06287 Da

IUPAC Name

(2R,3S,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol

Traditional Name

cladribine

CAS Registry Number

Not Available

SMILES

NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO)O3)C2=NC(Cl)=N1

InChI Identifier

InChI=1S/C10H12ClN5O3/c11-10-14-8(12)7-9(15-10)16(3-13-7)6-1-4(18)5(2-17)19-6/h3-6,17-18H,1-2H2,(H2,12,14,15)/t4-,5+,6+/m0/s1

InChI Key

PTOAARAWEBMLNO-KVQBGUIXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2'-deoxyribonucleosides

Direct Parent

Purine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside
6-aminopurine
Imidazopyrimidine
Purine
Aminopyrimidine
2-halopyrimidine
Halopyrimidine
N-substituted imidazole
Aryl chloride
Aryl halide
Pyrimidine
Imidolactam
Tetrahydrofuran
Heteroaromatic compound
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organohalogen compound
Primary alcohol
Primary amine
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organochlorine compound (CHEBI:567361 )
purine 2'-deoxyribonucleoside (CHEBI:567361 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.12	ALOGPS
logP	-0.28	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	1.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	119.31 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	67.18 m³·mol⁻¹	ChemAxon
Polarizability	25.93 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0014387

DrugBank ID

DB00242

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

19105

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cladribine

METLIN ID

Not Available

PubChem Compound

20279

PDB ID

CL9

ChEBI ID

567361

Good Scents ID

Not Available

References

General References

Kantarjian HM, Jeha S, Gandhi V, Wess M, Faderl S: Clofarabine: past, present, and future. Leuk Lymphoma. 2007 Oct;48(10):1922-30. doi: 10.1080/10428190701545644. [PubMed:17852710 ]
Larson ML, Venugopal P: Clofarabine: a new treatment option for patients with acute myeloid leukemia. Expert Opin Pharmacother. 2009 Jun;10(8):1353-7. doi: 10.1517/14656560902997990. [PubMed:19463072 ]
Zhenchuk A, Lotfi K, Juliusson G, Albertioni F: Mechanisms of anti-cancer action and pharmacology of clofarabine. Biochem Pharmacol. 2009 Dec 1;78(11):1351-9. doi: 10.1016/j.bcp.2009.06.094. Epub 2009 Jul 1. [PubMed:19576186 ]
LOTUS database [Link]

Showing NP-Card for cladribine (NP0213507)

MOL for NP0213507 (cladribine)

3D MOL for NP0213507 (cladribine)

3D SDF for NP0213507 (cladribine)

3D-SDF for NP0213507 (cladribine)

PDB for NP0213507 (cladribine)

3D PDB for NP0213507 (cladribine)

SMILES for NP0213507 (cladribine)

INCHI for NP0213507 (cladribine)

Structure for NP0213507 (cladribine)

3D Structure for NP0213507 (cladribine)