Structure of PDB 6oxd Chain A Binding Site BS02
Receptor Information
>6oxd Chain A (length=736) Species:
1773
(Mycobacterium tuberculosis) [
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PVIGSFAGVPLHSERAAQSPTEAAVHTHVAAAAAAHGYTPEQLVWHTPEG
IDVTPVYIAADRAAAEAEGYPLHSFPGEPPFVRGPYPTMYVNQPWTIRQY
AGFSTAADSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVQGDVGMA
GVAIDSILDMRQLFDGIDLSTVSVSMTMNGAVLPILALYVVAAEEQGVAP
EQLAGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAYTSAKMPKFNSIS
ISGYHIQEAGATADLELAYTLADGVDYIRAGLNAGLDIDSFAPRLSFFWG
IGMNFFMEVAKLRAGRLLWSELVAQFAPKSAKSLSLRTHSQTSGWSLTAQ
DVFNNVARTCIEAMAATQGHTQSLHTNALDEALALPTDFSARIARNTQLV
LQQESGTTRPIDPWGGSYYVEWLTHRLARRARAHIAEVAEHGGMAQAISD
GIPKLRIEEAAARTQARIDSGQQPVVGVNKYQVPEDHEIEVLKVENSRVR
AEQLAKLQRLRAGRDEPAVRAALAELTRAAAELGNNLLALAIDAARAQAT
VGEISEALEKVYGRHRAEIRTISGVYRDEVGKAPNIAAATELVEKFAEAD
GRRPRILIAKMGQDGHDRGQKVIATAFADIGFDVDVGSLFSTPEEVARQA
ADNDVHVIGVSSLAAGHLTLVPALRDALAQVGRPDIMIVVGGVIPPGDFD
ELYAAGATAIFPPGTVIADAAIDLLHRLAERLGYTL
Ligand information
Ligand ID
NJS
InChI
InChI=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
InChIKey
SJCVDYMGDNNJTF-BIBYKGKUSA-N
SMILES
Software
SMILES
CACTVS 3.385
C/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 2.0.7
CC(=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 12.01
C/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 2.0.7
C/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 3.385
CC(=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
Formula
C26 H42 N7 O19 P3 S
Name
Itaconyl coenzyme A
ChEMBL
DrugBank
ZINC
PDB chain
6oxd Chain A Residue 1002 [
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Receptor-Ligand Complex Structure
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PDB
6oxd
Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Resolution
2.0 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 score
3
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
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:6oxd
,
PDBe:6oxd
,
PDBj:6oxd
PDBsum
6oxd
PubMed
31672889
UniProt
P9WJK5
|MUTB_MYCTU Probable methylmalonyl-CoA mutase large subunit (Gene Name=mutB)
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