Structure of PDB 5vxo Chain B Binding Site BS01

Receptor Information
>5vxo Chain B (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
Global viewLocal viewStructure summary

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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)		M318 D320
Binding residue
(residue number reindexed from 1)		M279 D281
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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