Structure of PDB 6zjb Chain A Binding Site BS01

Receptor Information
>6zjb Chain A (length=217) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SARLLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIG
VLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALD
RAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDL
TGEPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNK
IWPYVYAFLQTKVPQRS
Ligand information
Ligand IDG5P
InChIInChI=1S/C20H29N10O23P5/c21-14-8-15(24-3-23-14)29(4-25-8)18-12(33)10(31)6(48-18)1-46-54(36,37)50-56(40,41)52-58(44,45)53-57(42,43)51-55(38,39)47-2-7-11(32)13(34)19(49-7)30-5-26-9-16(30)27-20(22)28-17(9)35/h3-7,10-13,18-19,31-34H,1-2H2,(H,36,37)(H,38,39)(H,40,41)(H,42,43)(H,44,45)(H2,21,23,24)(H3,22,27,28,35)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
InChIKeyCNMILLPGDWDFCZ-INFSMZHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
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)O[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
FormulaC20 H29 N10 O23 P5
NameP1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000261495500
PDB chain6zjb 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6zjb Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.
Resolution1.822 Å
Binding residue
(original residue number in PDB)		P16 G17 G19 K20 G21 T22 S38 I60 K64 L65 I66 M71 G91 R94 Q98 R124 R128 V137 N139 F142 R161 R172 E200 T201
Binding residue
(residue number reindexed from 1)		P13 G14 G16 K17 G18 T19 S35 I57 K61 L62 I63 M68 G88 R91 Q95 R121 R125 V134 N136 F139 R158 R169 E197 T198
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K20 R94 R128 R161 R172
Catalytic site (residue number reindexed from 1) K17 R91 R125 R158 R169
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zjb, PDBe:6zjb, PDBj:6zjb
PDBsum6zjb
PubMed32822537
UniProtQ9UIJ7|KAD3_HUMAN GTP:AMP phosphotransferase AK3, mitochondrial (Gene Name=AK3)

[Back to BioLiP]