NP-MRD: Showing NP-Card for (-)-Leptoclinidamine C (NP0081440)

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Record Information

Version

2.0

Created at

2022-04-29 02:25:53 UTC

Updated at

2022-04-29 02:25:53 UTC

NP-MRD ID

NP0081440

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Leptoclinidamine C

Description

(-)-Leptoclinidamine C is found in Leptoclinides durus.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292204252D          

 27 29  0  0  1  0            999 V2000
   -0.7217    7.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0853    6.8979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3402    6.1133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2118    5.5002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0188    5.6717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    6.4563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4313    4.9572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8792    4.3441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1256    4.6797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    4.2672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    4.6797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    3.4422    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    3.0297    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3034    2.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    1.7922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1648    2.1277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168    1.5147    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3043    0.8002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5027    0.9717    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1158    0.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5373    1.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3363    2.9347    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1209    3.1897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178    3.4422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178    4.2672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7323    3.0297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9766    7.8540    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
 18 19  4  0  0  0  0
 15 19  4  0  0  0  0
 19 20  1  0  0  0  0
 17 21  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  1  0  0  0  0
 13 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  1 27  1  0  0  0  0
M  END


  Mrv1652304292204252D          

 27 29  0  0  1  0            999 V2000
   -0.7217    7.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0853    6.8979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3402    6.1133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2118    5.5002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0188    5.6717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737    6.4563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4313    4.9572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8792    4.3441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1256    4.6797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    4.2672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    4.6797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    3.4422    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3034    3.0297    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3034    2.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    1.7922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1648    2.1277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168    1.5147    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3043    0.8002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5027    0.9717    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1158    0.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5373    1.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3363    2.9347    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1209    3.1897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178    3.4422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178    4.2672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7323    3.0297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9766    7.8540    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  4  0  0  0  0
 16 17  4  0  0  0  0
 17 18  4  0  0  0  0
 18 19  4  0  0  0  0
 15 19  4  0  0  0  0
 19 20  1  0  0  0  0
 17 21  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  1  0  0  0  0
 13 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  1 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081440

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSc1c(C[C@H](NC(=O)C2=CNC3=CC(Br)=CC=C23)C(O)=O)n(C)cn1C

> <INCHI_IDENTIFIER>
InChI=1S/C18H20BrN4O3S/c1-22-9-23(2)17(27-3)15(22)7-14(18(25)26)21-16(24)12-8-20-13-6-10(19)4-5-11(12)13/h4-6,8-9,14,20H,7H2,1-3H3,(H,21,24)(H,25,26)/t14-/m0/s1

> <INCHI_KEY>
YHMOPOJQUXUQIT-AWEZNQCLSA-N

> <FORMULA>
C18H20BrN4O3S

> <MOLECULAR_WEIGHT>
452.35

> <EXACT_MASS>
451.04395

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
43.141727266854716

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-2-[(6-bromo-1H-indol-3-yl)formamido]-3-[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]propanoic acid

> <ALOGPS_LOGP>
1.26

> <JCHEM_LOGP>
3.377311507999999

> <ALOGPS_LOGS>
-3.44

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.892191547370889

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.418485972931077

> <JCHEM_PKA_STRONGEST_BASIC>
-1.8255709644798404

> <JCHEM_POLAR_SURFACE_AREA>
92.05

> <JCHEM_REFRACTIVITY>
108.73469999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-[(6-bromo-1H-indol-3-yl)formamido]-3-[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      -1.347  13.196   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.159  12.876   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.635  11.411   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.395  10.267   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.902  10.587   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.378  12.052   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -2.672   9.253   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.641   8.109   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.234   8.735   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.099   7.965   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.433   8.735   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       1.099   6.425   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.433   5.655   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.433   4.115   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.099   3.345   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.308   3.972   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -1.338   2.827   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -0.568   1.494   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.938   1.814   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       2.083   0.783   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.870   2.988   0.000  0.00  0.00           C+0
HETATM   22  S   UNK     0      -0.628   5.478   0.000  0.00  0.00           S+0
HETATM   23  C   UNK     0      -2.092   5.954   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.767   6.425   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       3.767   7.965   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.100   5.655   0.000  0.00  0.00           O+0
HETATM   27 Br   UNK     0      -1.823  14.661   0.000  0.00  0.00          Br+0
CONECT    1    2    6   27                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   24                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   15   20                                                  
CONECT   20   19                                                            
CONECT   21   17                                                            
CONECT   22   16   23                                                       
CONECT   23   22                                                            
CONECT   24   13   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27    1                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₂₀BrN₄O₃S

Average Mass

452.3500 Da

Monoisotopic Mass

451.04395 Da

IUPAC Name

(2S)-2-[(6-bromo-1H-indol-3-yl)formamido]-3-[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]propanoic acid

Traditional Name

(2S)-2-[(6-bromo-1H-indol-3-yl)formamido]-3-[1,3-dimethyl-5-(methylsulfanyl)imidazol-4-yl]propanoic acid

CAS Registry Number

Not Available

SMILES

CSc1c(C[C@H](NC(=O)C2=CNC3=CC(Br)=CC=C23)C(O)=O)n(C)cn1C

InChI Identifier

InChI=1S/C18H20BrN4O3S/c1-22-9-23(2)17(27-3)15(22)7-14(18(25)26)21-16(24)12-8-20-13-6-10(19)4-5-11(12)13/h4-6,8-9,14,20H,7H2,1-3H3,(H,21,24)(H,25,26)/t14-/m0/s1

InChI Key

YHMOPOJQUXUQIT-AWEZNQCLSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Leptoclinides durus	Animalia	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	1.26	ALOGPS
logP	3.38	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	3.42	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	92.05 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	108.73 m³·mol⁻¹	ChemAxon
Polarizability	43.14 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	Yes	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Leptoclinidamine C (NP0081440)

MOL for NP0081440 ((-)-Leptoclinidamine C)

3D MOL for NP0081440 ((-)-Leptoclinidamine C)

3D SDF for NP0081440 ((-)-Leptoclinidamine C)

3D-SDF for NP0081440 ((-)-Leptoclinidamine C)

PDB for NP0081440 ((-)-Leptoclinidamine C)

3D PDB for NP0081440 ((-)-Leptoclinidamine C)

SMILES for NP0081440 ((-)-Leptoclinidamine C)

INCHI for NP0081440 ((-)-Leptoclinidamine C)

Structure for NP0081440 ((-)-Leptoclinidamine C)

3D Structure for NP0081440 ((-)-Leptoclinidamine C)