Structure of PDB 6oxd Chain A Binding Site BS02

Receptor Information
>6oxd Chain A (length=736) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVIGSFAGVPLHSERAAQSPTEAAVHTHVAAAAAAHGYTPEQLVWHTPEG
IDVTPVYIAADRAAAEAEGYPLHSFPGEPPFVRGPYPTMYVNQPWTIRQY
AGFSTAADSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVQGDVGMA
GVAIDSILDMRQLFDGIDLSTVSVSMTMNGAVLPILALYVVAAEEQGVAP
EQLAGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAYTSAKMPKFNSIS
ISGYHIQEAGATADLELAYTLADGVDYIRAGLNAGLDIDSFAPRLSFFWG
IGMNFFMEVAKLRAGRLLWSELVAQFAPKSAKSLSLRTHSQTSGWSLTAQ
DVFNNVARTCIEAMAATQGHTQSLHTNALDEALALPTDFSARIARNTQLV
LQQESGTTRPIDPWGGSYYVEWLTHRLARRARAHIAEVAEHGGMAQAISD
GIPKLRIEEAAARTQARIDSGQQPVVGVNKYQVPEDHEIEVLKVENSRVR
AEQLAKLQRLRAGRDEPAVRAALAELTRAAAELGNNLLALAIDAARAQAT
VGEISEALEKVYGRHRAEIRTISGVYRDEVGKAPNIAAATELVEKFAEAD
GRRPRILIAKMGQDGHDRGQKVIATAFADIGFDVDVGSLFSTPEEVARQA
ADNDVHVIGVSSLAAGHLTLVPALRDALAQVGRPDIMIVVGGVIPPGDFD
ELYAAGATAIFPPGTVIADAAIDLLHRLAERLGYTL
Ligand information
Ligand IDNJS
InChIInChI=1S/C26H42N7O19P3S/c1-13(25(39)40)8-16(35)56-7-6-28-15(34)4-5-29-23(38)20(37)26(2,3)10-49-55(46,47)52-54(44,45)48-9-14-19(51-53(41,42)43)18(36)24(50-14)33-12-32-17-21(27)30-11-31-22(17)33/h8,11-12,14-15,18-20,24,28,34,36-37H,4-7,9-10H2,1-3H3,(H,29,38)(H,39,40)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/b13-8-/t14-,15+,18-,19-,20+,24-/m1/s1
InChIKeySJCVDYMGDNNJTF-BIBYKGKUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C/C(=C/C(=O)SCCN[C@@H](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)C(O)=O
OpenEye OEToolkits 2.0.7CC(=CC(=O)SCCNC(CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)O)C(=O)O
ACDLabs 12.01C/C(C(=O)O)=C/C(=O)SCCNC(O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O
OpenEye OEToolkits 2.0.7C/C(=C/C(=O)SCCN[C@H](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)O)/C(=O)O
CACTVS 3.385CC(=CC(=O)SCCN[CH](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)C(O)=O
FormulaC26 H42 N7 O19 P3 S
NameItaconyl coenzyme A
ChEMBL
DrugBank
ZINC
PDB chain6oxd Chain A Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6oxd Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
Y91 T93 M94 Q98 T101 R103 Y105 S180 T182 T211 R223 H260 R299 S301 F303 R342 T343 H344 Q346 Q377
Binding residue
(residue number reindexed from 1)
Y86 T88 M89 Q93 T96 R98 Y100 S175 T177 T206 R218 H255 R294 S296 F298 R337 T338 H339 Q341 Q372
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Y105 Y259 H260 K623 D627 H629
Catalytic site (residue number reindexed from 1) Y100 Y254 H255 K610 D614 H616
Enzyme Commision number 5.4.99.2: methylmalonyl-CoA mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004494 methylmalonyl-CoA mutase activity
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
Biological Process
GO:0019678 propionate metabolic process, methylmalonyl pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6oxd, PDBe:6oxd, PDBj:6oxd
PDBsum6oxd
PubMed31672889
UniProtP9WJK5|MUTB_MYCTU Probable methylmalonyl-CoA mutase large subunit (Gene Name=mutB)

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