Structure of PDB 3wb2 Chain D Binding Site BS01

Receptor Information

>3wb2 Chain D (length=160) Species: 243232 (Methanocaldococcus jannaschii DSM 2661)

VVMEEIIKKAFIESINNIRRGDKEEELKKIQEKIVNAKKIVVATNNQKKF
KVIRDIMLRVCNAEIKMLDIDTRFADLTRMPALTKGLIALDIEKADLYIA
RGRLGAPGSGSMLVILDEKGRVLTASLSPSSVIHKEDIEERIKKELIEAL
SRIGISILEH

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: 3wb2 Chain C Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3wb2 Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis.
• Resolution: 2.44 Å
• Binding residue (original residue number in PDB): R102 R104 G111 S132 H135
• Binding residue (residue number reindexed from 1): R101 R103 G110 S131 H134
• Annotation score: 1

External links

• PDB: RCSB:3wb2, PDBe:3wb2, PDBj:3wb2
• PDBsum: 3wb2
• PubMed: 24249552
• UniProt: Q57912|Y488_METJA Uncharacterized protein MJ0488 (Gene Name=MJ0488)