Structure of PDB 6zjd Chain A Binding Site BS01

Receptor Information
>6zjd Chain A (length=214) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVL
AKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALDRA
YQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTG
EPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNKIW
PYVYAFLQTKVPQR
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain6zjd Chain A Residue 301 [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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PDB6zjd Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		S38 G39 L42 R43 L65 I66 M71 R94 Q98 R172
Binding residue
(residue number reindexed from 1)		S33 G34 L37 R38 L60 I61 M66 R89 Q93 R167
Annotation score4
Binding affinityMOAD: Kd=13uM
Enzymatic activity
Catalytic site (original residue number in PDB) K20 R94 R128 R161 R172
Catalytic site (residue number reindexed from 1) K15 R89 R123 R156 R167
Enzyme Commision number 2.7.4.10: nucleoside-triphosphate--adenylate kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0016874 ligase activity
GO:0019205 nucleobase-containing compound kinase activity
GO:0046899 nucleoside triphosphate adenylate kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006172 ADP biosynthetic process
GO:0007596 blood coagulation
GO:0009117 nucleotide metabolic process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
GO:0046033 AMP metabolic process
GO:0046039 GTP metabolic process
GO:0046041 ITP metabolic process
GO:0046051 UTP metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6zjd, PDBe:6zjd, PDBj:6zjd
PDBsum6zjd
PubMed32822537
UniProtQ9UIJ7|KAD3_HUMAN GTP:AMP phosphotransferase AK3, mitochondrial (Gene Name=AK3)

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