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Showing NP-Card for Corrinoid (NP0338983)

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Record Information
Version2.0
Created at2024-09-11 19:05:51 UTC
Updated at2024-09-11 19:05:51 UTC
NP-MRD IDNP0338983
Secondary Accession NumbersNone
Natural Product Identification
Common NameCorrinoid
Description Corrinoid was first documented in 2023 (PMID: 38010547). Based on a literature review very few articles have been published on Corrinoid (PMID: 38147780) (PMID: 38113523) (PMID: 37986477) (PMID: 37923808).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0338983 (Corrinoid)


  Mrv2104 05262321382D          

 23 27  0  0  0  0            999 V2000
    1.8527   -0.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6460   -0.3360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1066    0.3484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5979    0.9980    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8230    0.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0459    1.4410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2526    1.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2229    2.4920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9978    2.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4483    3.7384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1474    4.1764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556    4.9417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2786    4.8851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791    4.0848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3901    3.5361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7527    2.7950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4815    2.4086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3392    1.5959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5224    1.4802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1599    2.2213    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8815    0.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7800    3.6468    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5065    2.1255    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  4  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  4  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21  3  1  4  0  0  0
 14 22  2  0  0  0  0
 11 22  1  0  0  0  0
  9 23  2  0  0  0  0
  6 23  1  0  0  0  0
M  END
Download

3D MOL for NP0338983 (Corrinoid)

Download
3D SDF for NP0338983 (Corrinoid)

  Mrv2104 05262321382D          

 23 27  0  0  0  0            999 V2000
    1.8527   -0.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6460   -0.3360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1066    0.3484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5979    0.9980    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8230    0.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0459    1.4410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2526    1.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2229    2.4920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9978    2.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4483    3.7384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1474    4.1764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4556    4.9417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2786    4.8851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4791    4.0848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3901    3.5361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7527    2.7950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4815    2.4086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3392    1.5959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5224    1.4802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1599    2.2213    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8815    0.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7800    3.6468    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5065    2.1255    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  4  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  4  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21  3  1  4  0  0  0
 14 22  2  0  0  0  0
 11 22  1  0  0  0  0
  9 23  2  0  0  0  0
  6 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0338983

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C1CC2=NC1C1CCC(C=C3CCC(C=C4CCC(N4)=C2)=N3)=N1

> <INCHI_IDENTIFIER>
InChI=1/C19H22N4/c1-3-14-10-16-5-7-18(22-16)19-8-6-17(23-19)11-15-4-2-13(21-15)9-12(1)20-14/h9-11,18-20H,1-8H2

> <INCHI_KEY>
PXOPDYTVWWQZEK-UHFFFAOYNA-N

> <FORMULA>
C19H22N4

> <MOLECULAR_WEIGHT>
306.413

> <EXACT_MASS>
306.184446724

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
35.43032030348141

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10,12(21),15,17(20)-hexaene

> <JCHEM_LOGP>
1.4788589826666656

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
19.234881092871206

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.8251394799778

> <JCHEM_PKA_STRONGEST_BASIC>
9.557342010120722

> <JCHEM_POLAR_SURFACE_AREA>
49.11

> <JCHEM_REFRACTIVITY>
96.04129999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10,12(21),15,17(20)-hexaene

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0338983 (Corrinoid)
Download
PDB for NP0338983 (Corrinoid)
HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0       3.458  -0.205   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.939  -0.627   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.799   0.650   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.849   1.863   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       3.403   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.952   2.690   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.472   3.113   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.416   4.652   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.863   5.180   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.703   6.978   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.008   7.796   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.584   9.225   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.120   9.119   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.494   7.625   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.195   6.601   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.872   5.217   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.232   4.496   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.967   2.979   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.442   2.763   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       7.765   4.146   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       7.245   1.179   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       5.189   6.807   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       2.812   3.968   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   23                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   23                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   22                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19   16                                                       
CONECT   21   19    3                                                       
CONECT   22   14   11                                                       
CONECT   23    9    6                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   54    0
END

Download
3D PDB for NP0338983 (Corrinoid)
Download
SMILES for NP0338983 (Corrinoid)
C1CC2=NC1C1CCC(C=C3CCC(C=C4CCC(N4)=C2)=N3)=N1
Download
INCHI for NP0338983 (Corrinoid)
InChI=1/C19H22N4/c1-3-14-10-16-5-7-18(22-16)19-8-6-17(23-19)11-15-4-2-13(21-15)9-12(1)20-14/h9-11,18-20H,1-8H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC19H22N4
Average Mass306.4130 Da
Monoisotopic Mass306.18445 Da
IUPAC Name20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10,12(21),15,17(20)-hexaene
Traditional Name20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10,12(21),15,17(20)-hexaene
CAS Registry NumberNot Available
SMILES
C1CC2=NC1C1CCC(C=C3CCC(C=C4CCC(N4)=C2)=N3)=N1
InChI Identifier
InChI=1/C19H22N4/c1-3-14-10-16-5-7-18(22-16)19-8-6-17(23-19)11-15-4-2-13(21-15)9-12(1)20-14/h9-11,18-20H,1-8H2
InChI KeyPXOPDYTVWWQZEK-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.48ChemAxon
pKa (Strongest Acidic)17.83ChemAxon
pKa (Strongest Basic)9.56ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.11 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity96.04 m³·mol⁻¹ChemAxon
Polarizability35.43 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCorrinoid  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Rahmatullah R, Marquis CP: Evaluation of alternate hosts for recombinant expression of a reductive dehalogenase. Enzyme Microb Technol. 2024 Mar;174:110390. doi: 10.1016/j.enzmictec.2023.110390.  Epub 2023 Dec 22. [PubMed:38147780  ] 
  2. Liu G, Chen K, Wu Z, Ji Y, Lu L, Liu S, Li ZL, Ji R, Liu SJ, Jiang J, Qiao W: Genome-Centric Metatranscriptomic Characterization of a Humin-Facilitated Anaerobic Tetrabromobisphenol A-Dehalogenating Consortium. Environ Sci Technol. 2024 Jan 16;58(2):1299-1311. doi: 10.1021/acs.est.3c06118.  Epub 2023 Dec 19. [PubMed:38113523  ] 
  3. Arya CK, Maurya S, Ramanathan G: Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides. Environ Sci Pollut Res Int. 2023 Dec;30(60):125947-125964. doi:  10.1007/s11356-023-30858-1. Epub 2023 Nov 27. [PubMed:38010547  ] 
  4. Ashagrie H, Baye K, Guibert B, Seyoum Y, Rochette I, Humblot C: Cereal-based fermented foods as a source of folate and cobalamin: The role of endogenous microbiota. Food Res Int. 2023 Dec;174(Pt 1):113625. doi: 10.1016/j.foodres.2023.113625. Epub  2023 Oct 27. [PubMed:37986477  ] 
  5. Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J: Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun. 2023 Nov 3;14(1):7038. doi: 10.1038/s41467-023-42927-7. [PubMed:37923808  ]