Structure of PDB 3dbd Chain A Binding Site BS01

Receptor Information
>3dbd Chain A (length=261) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKS
MLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRS
LLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDD
MDVKIGDFGLATKIHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRI
KKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMR
LPTSCLTVPPR
Ligand information
Ligand ID3FR
InChIInChI=1S/C28H24ClN5O/c1-17(19-8-4-3-5-9-19)32-27-15-26-25(16-31-27)18(2)33-34(26)22-13-20(12-21(29)14-22)23-10-6-7-11-24(23)28(30)35/h3-17H,1-2H3,(H2,30,35)(H,31,32)/t17-/m0/s1
InChIKeyIFCBXJXWEYHVPY-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C@H](Nc1cc2n(nc(C)c2cn1)c3cc(Cl)cc(c3)c4ccccc4C(N)=O)c5ccccc5
ACDLabs 10.04O=C(N)c1ccccc1c2cc(cc(Cl)c2)n5nc(c3c5cc(nc3)NC(c4ccccc4)C)C
OpenEye OEToolkits 1.5.0Cc1c2cnc(cc2n(n1)c3cc(cc(c3)Cl)c4ccccc4C(=O)N)NC(C)c5ccccc5
OpenEye OEToolkits 1.5.0Cc1c2cnc(cc2n(n1)c3cc(cc(c3)Cl)c4ccccc4C(=O)N)N[C@@H](C)c5ccccc5
CACTVS 3.341C[CH](Nc1cc2n(nc(C)c2cn1)c3cc(Cl)cc(c3)c4ccccc4C(N)=O)c5ccccc5
FormulaC28 H24 Cl N5 O
Name3'-chloro-5'-(3-methyl-6-{[(1S)-1-phenylethyl]amino}-1H-pyrazolo[4,3-c]pyridin-1-yl)biphenyl-2-carboxamide;
3'-chloro-5'-[3-methyl-6-(1-phenyl-ethylamino)-pyrazolo[4,3-c]pyridin-1-yl]-biphenyl-2-carboxylic acid amide
ChEMBL
DrugBank
ZINCZINC000034285228
PDB chain3dbd 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

[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]
PDB3dbd Design and synthesis of 2-amino-pyrazolopyridines as Polo-like kinase 1 inhibitors.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		L45 K47 C53 K68 L116 C119 R122 F169
Binding residue
(residue number reindexed from 1)		L22 K24 C30 K45 L93 C96 R99 F146
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.38,IC50=42nM
Enzymatic activity
Catalytic site (original residue number in PDB) D162 K164 G166 N167 D180
Catalytic site (residue number reindexed from 1) D139 K141 G143 N144 D157
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:3dbd, PDBe:3dbd, PDBj:3dbd
PDBsum3dbd
PubMed18793847
UniProtQ4KMI8

[Back to BioLiP]