Structure of PDB 5vxc Chain A Binding Site BS01

Receptor Information
>5vxc Chain A (length=301) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HKYIPRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLR
IVKTLEDIDLGPTEKCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVE
SPEEIQWFADKFSFHLKGRKLEQPMNLIPFVETAMGLLNFKAVCEETLKV
GPQVGLFLDAVVFGGEDFRASIGATSSKETLDILYARQKIVVIAKAFGLQ
AIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQEQFSPSPE
KIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSIKE
K
Ligand information
Ligand IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(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@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain5vxc Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vxc The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
Resolution1.872 Å
Binding residue
(original residue number in PDB)		Y50 K57 K58 K61 R107 I272 H273 P274
Binding residue
(residue number reindexed from 1)		Y11 K18 K19 K22 R68 I233 H234 P235
Annotation score3
Enzymatic activity
Enzyme Commision number 2.3.3.-
2.3.3.9: malate synthase.
3.1.2.30: (3S)-malyl-CoA thioesterase.
4.1.3.25: (S)-citramalyl-CoA lyase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004474 malate synthase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0047777 (S)-citramalyl-CoA lyase activity
Biological Process
GO:0070207 protein homotrimerization
GO:0106064 regulation of cobalamin metabolic process
GO:0106121 positive regulation of cobalamin metabolic process
Cellular Component
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vxc, PDBe:5vxc, PDBj:5vxc
PDBsum5vxc
PubMed29056341
UniProtQ8N0X4|CLYBL_HUMAN Citramalyl-CoA lyase, mitochondrial (Gene Name=CLYBL)

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