Structure of PDB 4mbl Chain A Binding Site BS01

Receptor Information

>4mbl Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPN
GTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDF
ITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGEL
KLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILL
YDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFE
EIQNHPWMQDVLLPQETAEIHLHS

Ligand information

Ligand ID

26L

InChI

InChI=1S/C22H23N5/c23-19-7-3-4-8-20(19)25-21-11-12-27-22(26-21)18(14-24-27)17-10-9-15-5-1-2-6-16(15)13-17/h1-2,5-6,9-14,19-20H,3-4,7-8,23H2,(H,25,26)/t19-,20-/m1/s1

InChIKey

LODPYXJMYAQIRB-WOJBJXKFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1ccc2cc(ccc2c1)c3cnn4c3nc(cc4)NC5CCCCC5N
ACDLabs 12.01	n1c(ccn2ncc(c12)c4cc3ccccc3cc4)NC5CCCCC5N
CACTVS 3.385	N[CH]1CCCC[CH]1Nc2ccn3ncc(c4ccc5ccccc5c4)c3n2
OpenEye OEToolkits 1.7.6	c1ccc2cc(ccc2c1)c3cnn4c3nc(cc4)N[C@@H]5CCCC[C@H]5N
CACTVS 3.385	N[C@@H]1CCCC[C@H]1Nc2ccn3ncc(c4ccc5ccccc5c4)c3n2

Formula

C22 H23 N5

Name

(1R,2R)-N-[3-(naphthalen-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]cyclohexane-1,2-diamine

PDB chain

4mbl Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	4mbl Discovery of pyrazolo[1,5-a]pyrimidine-based Pim inhibitors: A template-based approach.
Resolution	2.6 Å
Binding residue (original residue number in PDB)	L44 F49 A65 K67 D128 L174 D186
Binding residue (residue number reindexed from 1)	L12 F17 A33 K35 D96 L142 D154
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=8.54,IC50=2.9nM BindingDB: IC50=2.9nM

Enzymatic activity

Catalytic site (original residue number in PDB)	D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1)	D135 K137 N140 D154 L161 T172
Enzyme Commision number	2.7.11.1: non-specific serine/threonine protein kinase.

Gene Ontology

	Molecular Function
GO:0004672	protein kinase activity
GO:0004674	protein serine/threonine kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008134	transcription factor binding
GO:0030145	manganese ion binding
GO:0043024	ribosomal small subunit binding
GO:0044024	histone H2AS1 kinase activity
GO:0046872	metal ion binding
GO:0106310	protein serine kinase activity

	Biological Process
GO:0006338	chromatin remodeling
GO:0006468	protein phosphorylation
GO:0006915	apoptotic process
GO:0016310	phosphorylation
GO:0022898	regulation of transmembrane transporter activity
GO:0043066	negative regulation of apoptotic process
GO:0043433	negative regulation of DNA-binding transcription factor activity
GO:0045824	negative regulation of innate immune response
GO:0045893	positive regulation of DNA-templated transcription
GO:0046777	protein autophosphorylation
GO:0050821	protein stabilization
GO:0060045	positive regulation of cardiac muscle cell proliferation
GO:0070561	vitamin D receptor signaling pathway
GO:0071346	cellular response to type II interferon
GO:0090336	positive regulation of brown fat cell differentiation
GO:1902033	regulation of hematopoietic stem cell proliferation
GO:1904263	positive regulation of TORC1 signaling
GO:1905062	positive regulation of cardioblast proliferation
GO:1990748	cellular detoxification

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005886	plasma membrane

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:4mbl, PDBe:4mbl, PDBj:4mbl
PDBsum	4mbl
PubMed	24091081
UniProt	P11309\|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

[Back to BioLiP]