Structure of PDB 4rkz Chain B Binding Site BS01

Receptor Information
>4rkz Chain B (length=318) Species: 273075 (Thermoplasma acidophilum DSM 1728) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMTYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRS
ETRIYADEATHIYFNGTESDNRSVRRVLDRYSSVFEEAFGTKTVSYSSQN
FGILSGSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGL
TITWSDGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDL
YPARKKHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVI
RENMQKLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFG
SKKKMLRIVGGAWHRRPE
Ligand information
Ligand ID3S4
InChIInChI=1S/C6H13O7P/c1-6(2-3-7,4-5(8)9)13-14(10,11)12/h7H,2-4H2,1H3,(H,8,9)(H2,10,11,12)/t6-/m1/s1
InChIKeyVWCNCYQNEAUWMQ-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(OC(CCO)(C)CC(=O)O)(O)O
OpenEye OEToolkits 1.7.6C[C@@](CCO)(CC(=O)O)OP(=O)(O)O
CACTVS 3.385C[C](CCO)(CC(O)=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.6CC(CCO)(CC(=O)O)OP(=O)(O)O
CACTVS 3.385C[C@@](CCO)(CC(O)=O)O[P](O)(O)=O
FormulaC6 H13 O7 P
Name(3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid
ChEMBL
DrugBank
ZINCZINC000114243420
PDB chain4rkz 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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PDB4rkz Structural analysis of mevalonate-3-kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L18 L19 S105 E140 R144 R185 T275
Binding residue
(residue number reindexed from 1)		L20 L21 S105 E140 R144 R185 T275
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.185: mevalonate 3-kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016310 phosphorylation
GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rkz, PDBe:4rkz, PDBj:4rkz
PDBsum4rkz
PubMed25422158
UniProtQ9HIN1|MV3K_THEAC Mevalonate 3-kinase (Gene Name=Ta1305)

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