Structure of PDB 5d4v Chain D Binding Site BS02

Receptor Information

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

EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNY
TAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNP
DLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAP
FIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIP
NLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLI
YSFVEEL

Ligand information

• Ligand ID: SAH
• InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
• InChIKey: ZJUKTBDSGOFHSH-WFMPWKQPSA-N
• SMILES:
  CACTVS 3.341: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
• Formula: C14 H20 N6 O5 S
• Name: S-ADENOSYL-L-HOMOCYSTEINE
• ChEMBL: CHEMBL418052
• DrugBank: DB01752
• ZINC: ZINC000004228232
• PDB chain: 5d4v Chain D Residue 301

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): Y56 L57 W58 D77 I78 L117 T118 I123 G184 T185
• Binding residue (residue number reindexed from 1): Y45 L46 W47 D66 I67 L106 T107 I112 G173 T174
• Annotation score: 4

External links

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