Structure of PDB 6wfh Chain A Binding Site BS02

Receptor Information

>6wfh Chain A (length=139) Species: 100226 (Streptomyces coelicolor A3(2))

SLTRIDHIGIACHDLDATVEFYRATYGFEVFHTEVNEEQGVREAMLKIND
TSDGGASYLQLLEPTREDSAVGKWLAKNGEGVHHIAFGTADVDADAADIR
DKGVRVLYDEPRRGSMGSRITFLHPKDCHGVLTELVTSA

Ligand information

• Ligand ID: V0V
• InChI: InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-11,13,16-18,22,34-35,39H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/b24-12+/t13-,16-,17-,18+,22-/m1/s1
• InChIKey: RERUYCLVCZLHGP-JXZMNPEQSA-N
• SMILES:
  CACTVS 3.385: C\C(C(O)=O)=C(O)/SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  CACTVS 3.385: CC(C(O)=O)=C(O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.7: CC(=C(O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)C(=O)O
  OpenEye OEToolkits 2.0.7: C/C(=C(/O)\SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)/C(=O)O
  ACDLabs 12.01: c3n(C1OC(C(C1O)OP(O)(O)=O)COP(O)(=O)OP(O)(OCC(C)(C)C(O)C(=O)NCCC(=O)NCCS/C(O)=C(/C(O)=O)C)=O)c2ncnc(c2n3)N
• Formula: C25 H40 N7 O19 P3 S
• Name: (3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name)
• PDB chain: 6wfh Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wfh Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase.
• Resolution: 1.84 Å
• Binding residue (original residue number in PDB): H7 Q39 Q60 A70 K73 W74 H83 H84 L107 G114 S115 F122 P125 K126 L132 E134
• Binding residue (residue number reindexed from 1): H7 Q39 Q60 A70 K73 W74 H83 H84 L107 G114 S115 F122 P125 K126 L132 E134
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): H7 E43 Q60 H84 E134
• Catalytic site (residue number reindexed from 1): H7 E43 Q60 H84 E134

Gene Ontology

Molecular Function

• GO:0004493 methylmalonyl-CoA epimerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0046491 L-methylmalonyl-CoA metabolic process

External links

• PDB: RCSB:6wfh, PDBe:6wfh, PDBj:6wfh
• PDBsum: 6wfh
• PubMed: 34856049
• UniProt: Q9L2C2