Structure of PDB 5d4v Chain D Binding Site BS01

Receptor Information

>5d4v Chain D (length=257) Species: 2190 (Methanocaldococcus jannaschii)

EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNY
TAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNP
DLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAP
FIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIP
NLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLI
YSFVEEL

Ligand information

• Ligand ID: YGP
• InChI: InChI=1S/C17H21N6O9P/c1-6-3-8(7(2)14(26)20-6)32-33(28,29)30-4-9-11(24)12(25)16(31-9)23-5-19-10-13(23)21-17(18)22-15(10)27/h3,5,9,11-12,16,24-25H,4H2,1-2H3,(H,20,26)(H,28,29)(H3,18,21,22,27)/t9-,11-,12-,16-/m1/s1
• InChIKey: SHYVQHDJQQBUQP-UBEDBUPSSA-N
• SMILES:
  CACTVS 3.385: CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N
  OpenEye OEToolkits 1.7.6: CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O
  ACDLabs 12.01: O=C4NC(=CC(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)=C4C)C
  OpenEye OEToolkits 1.7.6: CC1=CC(=C(C(=O)N1)C)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O
  CACTVS 3.385: CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N
• Formula: C17 H21 N6 O9 P
• Name: 5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine
• ZINC: ZINC000098209637
• PDB chain: 5d4v Chain C Residue 308

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d4v Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Y156 E266
• Binding residue (residue number reindexed from 1): Y145 E255
• Annotation score: 1

External links

• PDB: RCSB:5d4v, PDBe:5d4v, PDBj:5d4v
• PDBsum: 5d4v
• PubMed: 27391308
• UniProt: Q57913|Y489_METJA Uncharacterized protein MJ0489 (Gene Name=MJ0489)