Structure of PDB 3d5w Chain A Binding Site BS01

Receptor Information
>3d5w Chain A (length=285) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKS
MLPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLL
ELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDDMD
VKIGDFGLATKIEFDGERKKTLCGTPNYIAPEVLCKKGHSFEVDIWSLGC
ILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHAD
PTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPR
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 chain3d5w Chain A Residue 313 [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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PDB3d5w Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K47 A66 K68 C119 F169
Binding residue
(residue number reindexed from 1)		K24 A43 K45 C94 F144
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D162 K164 G166 N167 D180 T200
Catalytic site (residue number reindexed from 1) D137 K139 G141 N142 D155 T175
Enzyme Commision number 2.7.11.21: polo kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3d5w, PDBe:3d5w, PDBj:3d5w
PDBsum3d5w
PubMed18703838
UniProtQ4KMI8

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