Structure of PDB 5vxo Chain A Binding Site BS01

Receptor Information
>5vxo Chain A (length=298) 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
KIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSI
Ligand information
Ligand ID1VU
InChIInChI=1S/C24H40N7O17P3S/c1-4-15(33)52-8-7-26-14(32)5-6-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-13-18(47-49(37,38)39)17(34)23(46-13)31-12-30-16-20(25)28-11-29-21(16)31/h11-13,17-19,23,34-35H,4-10H2,1-3H3,(H,26,32)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t13-,17-,18-,19+,23-/m1/s1
InChIKeyQAQREVBBADEHPA-IEXPHMLFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCC(=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
CACTVS 3.385CCC(=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
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CC
CACTVS 3.385CCC(=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 1.7.6CCC(=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
FormulaC24 H40 N7 O17 P3 S
Namepropionyl Coenzyme A
ChEMBL
DrugBankDB02912
ZINCZINC000008551120
PDB chain5vxo Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vxo The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
Resolution2.266 Å
Binding residue
(original residue number in PDB)		Y50 K57 K58 K61 G77 R107 I272 H273 P274
Binding residue
(residue number reindexed from 1)		Y11 K18 K19 K22 G38 R68 I233 H234 P235
Annotation score4
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:5vxo, PDBe:5vxo, PDBj:5vxo
PDBsum5vxo
PubMed29056341
UniProtQ8N0X4|CLYBL_HUMAN Citramalyl-CoA lyase, mitochondrial (Gene Name=CLYBL)

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