Structure of PDB 6n92 Chain C Binding Site BS01

Receptor Information
>6n92 Chain C (length=260) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCI
ILRAPSGSKVFSAGHDIHELPSGGRDPLSYDDPLRQITRMIQKFPKPIIS
MVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRD
AGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEK
APLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFL
EKRKPNFVGH
Ligand information
Ligand IDKFV
InChIInChI=1S/C24H38N8O19P3S/c1-12(32(38)39)23(37)55-7-6-26-14(33)4-5-27-21(36)18(35)24(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)31-11-30-15-19(25)28-10-29-20(15)31/h10-11,13,16-18,22,34-35H,4-9H2,1-3H3,(H8-,25,26,27,28,29,33,36,37,38,39,40,41,42,43,44,45,46)/q-1/t13-,16-,17-,18+,22-/m1/s1
InChIKeyBLWVPDVKNPMTPY-ZSJPKINUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(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)=[N+]([O-])[O-]
ACDLabs 12.01n1cnc2c(c1N)ncn2C3C(O)C(C(O3)COP(OP(OCC(C(C(=O)NCCC(=O)NCCSC(\C(=[N+](\[O-])[O-])C)=O)O)(C)C)(=O)O)(O)=O)OP(O)(O)=O
OpenEye OEToolkits 2.0.7CC(=[N+]([O-])[O-])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
OpenEye OEToolkits 2.0.7CC(=[N+]([O-])[O-])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
CACTVS 3.385CC(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)=[N+]([O-])[O-]
FormulaC24 H38 N8 O19 P3 S
Name[1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium
ChEMBL
DrugBank
ZINC
PDB chain6n92 Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6n92 Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
K24 L25 A64 H66 D67 I68 H69 L71 W108 L136 V138 Y140 F250
Binding residue
(residue number reindexed from 1)
K23 L24 A63 H65 D66 I67 H68 L70 W107 L135 V137 Y139 F249
Annotation score2
Binding affinityMOAD: Ki=10.8uM
PDBbind-CN: -logKd/Ki=4.97,Ki=10.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) H66 L71 G110 E113 P133 V138 Y140 E228 Y238
Catalytic site (residue number reindexed from 1) H65 L70 G109 E112 P132 V137 Y139 E227 Y237
Enzyme Commision number 4.1.1.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004492 methyl/ethyl malonyl-CoA decarboxylase activity
GO:0016829 lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006635 fatty acid beta-oxidation
Cellular Component
GO:0005829 cytosol

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6n92, PDBe:6n92, PDBj:6n92
PDBsum6n92
PubMed30869886
UniProtP52045|SCPB_ECOLI Methylmalonyl-CoA decarboxylase (Gene Name=scpB)

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