Structure of PDB 7n9d Chain A Binding Site BS01

Receptor Information
>7n9d Chain A (length=253) Species: 1291540 (Methanomethylophilus alvi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMILIKLGGSVITDKSEYHKFNKETVSRLADEIRRSGQDVMVVHGAGSFG
HVIAKKYAIQDGHVDDGQIPAAARAMCDTRELSSMVVEELLAQGIPAVSV
APGSCFVMEDGKLIVDNEEPIRRLADLGIMPVMFGDVVPDRKKGFAIVSG
DQCMEVLCRMFDPEKVVFVSDIDGLYTADPKTDKKARLIGEVTRKKLALT
DITVADVTGGVHSKMEAMLRMTDRNRRCYLVNGNAPNRLYSLLKGETVTC
TVA
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 chain7n9d Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7n9d Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus .
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G7 G8 S9 K14 S169 D170 I171 Y175 A177 D178 D202 G211 V212 K215
Binding residue
(residue number reindexed from 1)		G8 G9 S10 K15 S170 D171 I172 Y176 A178 D179 D201 G210 V211 K214
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.26: isopentenyl phosphate kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0102043 isopentenyl phosphate kinase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7n9d, PDBe:7n9d, PDBj:7n9d
PDBsum7n9d
PubMed34905349
UniProtM9SEQ1

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