Structure of PDB 1dvr Chain B Binding Site BS01

Receptor Information
>1dvr Chain B (length=220) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLG
LEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILVGFPRTIPQAEK
LDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPK
EDMKDDVTGEALVQISDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGV
DASQPPATVWADILNKLGKN
Ligand information
Ligand IDATF
InChIInChI=1S/C11H16F2N5O12P3/c12-11(13,31(21,22)23)32(24,25)30-33(26,27)28-1-4-6(19)7(20)10(29-4)18-3-17-5-8(14)15-2-16-9(5)18/h2-4,6-7,10,19-20H,1H2,(H,24,25)(H,26,27)(H2,14,15,16)(H2,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyODWAWOIUPXBZKQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O)O)N
ACDLabs 10.04FC(F)(P(=O)(O)O)P(=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)(C(F)(F)P(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)C(F)(F)[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H16 F2 N5 O12 P3
NamePHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1160358
DrugBank
ZINCZINC000015501787
PDB chain1dvr Chain A Residue 230 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dvr Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		K55 Q59
Binding residue
(residue number reindexed from 1)		K55 Q59
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K17 R93 R132 I165 R176
Catalytic site (residue number reindexed from 1) K17 R93 R132 I165 R176
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0003688 DNA replication origin binding
GO:0004017 adenylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0019205 nucleobase-containing compound kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006172 ADP biosynthetic process
GO:0006270 DNA replication initiation
GO:0009117 nucleotide metabolic process
GO:0016310 phosphorylation
GO:0036388 pre-replicative complex assembly
GO:0046033 AMP metabolic process
GO:0046034 ATP metabolic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
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:1dvr, PDBe:1dvr, PDBj:1dvr
PDBsum1dvr
PubMed8594191
UniProtP07170|KAD2_YEAST Adenylate kinase (Gene Name=ADK1)

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