Structure of PDB 3mp5 Chain B Binding Site BS01

Receptor Information
>3mp5 Chain B (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLPKRVKIVEVGPMDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFV
SPKWVPQMGDHTEVLKGIQKFPGINYPVLTPNLKGFEAAVAAGAKEVVIF
GAASELFTKKNINCSIEESFQRFDAILKAAQSANISVRGYVSCALGCPYE
GKISPAKVAEVTKKFYSMGCYEISLGDTIGVGTPGIMKDMLSAVMQEVPL
AALAVHCHDTYGQALANTLMALQMGVSVVDSSVAGLGGCPYAQGASGNLA
TEDLVYMLEGLGIHTGVNLQKLLEAGNFICQALNRKTSSKVAQATC
Ligand information
Ligand IDHMG
InChIInChI=1S/C27H44N7O20P3S/c1-26(2,21(40)24(41)30-5-4-15(35)29-6-7-58-17(38)9-27(3,42)8-16(36)37)11-51-57(48,49)54-56(46,47)50-10-14-20(53-55(43,44)45)19(39)25(52-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,19-21,25,39-40,42H,4-11H2,1-3H3,(H,29,35)(H,30,41)(H,36,37)(H,46,47)(H,48,49)(H2,28,31,32)(H2,43,44,45)/p-5/t14-,19-,20-,21+,25-,27+/m1/s1
InChIKeyCABVTRNMFUVUDM-VRHQGPGLSA-I
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5C[C@](CC(=O)[O-])(CC(=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)O
CACTVS 3.385C[C@](O)(CC([O-])=O)CC(=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
CACTVS 3.385C[C](O)(CC([O-])=O)CC(=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
ACDLabs 12.01[O-]C(=O)CC(O)(C)CC(=O)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
OpenEye OEToolkits 1.7.5CC(C)(COP(=O)([O-])OP(=O)([O-])OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])C(C(=O)NCCC(=O)NCCSC(=O)CC(C)(CC(=O)[O-])O)O
FormulaC27 H39 N7 O20 P3 S
Name3-HYDROXY-3-METHYLGLUTARYL-COENZYME A;
(S)-HMG-COA
ChEMBL
DrugBankDB03169
ZINC
PDB chain3mp5 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mp5 Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		D42 Q45 S78 W81 F127 N138 N140 Y167 S169 T205 C266
Binding residue
(residue number reindexed from 1)		D15 Q18 S51 W54 F100 N111 N113 Y140 S142 T178 C239
Annotation score5
Enzymatic activity
Enzyme Commision number 4.1.3.4: hydroxymethylglutaryl-CoA lyase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004419 hydroxymethylglutaryl-CoA lyase activity
GO:0005198 structural molecule activity
GO:0016829 lyase activity
GO:0016833 oxo-acid-lyase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006552 L-leucine catabolic process
GO:0006629 lipid metabolic process
GO:0007005 mitochondrion organization
GO:0046951 ketone body biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3mp5, PDBe:3mp5, PDBj:3mp5
PDBsum3mp5
PubMed20558737
UniProtP35914|HMGCL_HUMAN Hydroxymethylglutaryl-CoA lyase, mitochondrial (Gene Name=HMGCL)

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