Structure of PDB 4rkz Chain A Binding Site BS01

Receptor Information
>4rkz Chain A (length=313) Species: 273075 (Thermoplasma acidophilum DSM 1728) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYRSIGSTAYPTIGVVLLGGIANPVTRTPLHTSAGIAYSDSCGSIRSETR
IYADEATHIYFNGTESTSVRRVLDRYSSVFEEAFGTKTVSYSSQNFGILS
GSSDAGAASIGAAILGLKPDLDPHDVENDLRAVSESAGRSLFGGLTITWS
DGFHAYTEKILDPEAFSGYSIVAFAFDYQRNPSDVIHQNIVRSDLYPARK
KHADEHAHMIKEYAKTNDIKGIFDLAQEDTEEYHSILRGVGVNVIRENMQ
KLISYLKLIRKDYWNAYIVTGGSNVYVAVESENADRLFSIENTFGSKKKM
LRIVGGAWHRRPE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4rkz Chain A Residue 401 [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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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)		F62 Y96 S98 N100 S105 G106 S107 S108 G111 R185 S188
Binding residue
(residue number reindexed from 1)		F61 Y91 S93 N95 S100 G101 S102 S103 G106 R180 S183
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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