Structure of PDB 3kad Chain A Binding Site BS01

Receptor Information
>3kad Chain A (length=145) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPPGWEKAMSRSSGRVYYFNHITNASQWERPSEPARVRCSHLLVKHSQSR
RPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKA
RGDLGAFSRGQMAKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Ligand information
Ligand ID4C0
InChIInChI=1S/C19H19N3O3/c23-18(11-10-13-6-2-1-3-7-13)22-16(19(24)25)12-17-20-14-8-4-5-9-15(14)21-17/h1-9,16H,10-12H2,(H,20,21)(H,22,23)(H,24,25)/t16-/m1/s1
InChIKeyAZXJPZVGZBWZMA-MRXNPFEDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(cc1)CCC(=O)N[C@H](Cc2[nH]c3ccccc3n2)C(=O)O
CACTVS 3.352OC(=O)[CH](Cc1[nH]c2ccccc2n1)NC(=O)CCc3ccccc3
OpenEye OEToolkits 1.7.0c1ccc(cc1)CCC(=O)NC(Cc2[nH]c3ccccc3n2)C(=O)O
CACTVS 3.352OC(=O)[C@@H](Cc1[nH]c2ccccc2n1)NC(=O)CCc3ccccc3
ACDLabs 11.02O=C(O)C(NC(=O)CCc1ccccc1)Cc3nc2ccccc2n3
FormulaC19 H19 N3 O3
Name3-(1H-benzimidazol-2-yl)-N-(3-phenylpropanoyl)-D-alanine;
(R)-3-(1H-Benzoimidazol-2-yl)-2-(3-phenyl-propionylamino)-propionic acid
ChEMBLCHEMBL595949
DrugBank
ZINCZINC000045350154
PDB chain3kad Chain A Residue 164 [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]
PDB3kad Structure-guided design of alpha-amino acid-derived Pin1 inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		H59 L61 K63 R69 C113 S115 L122 F134 S154 H157
Binding residue
(residue number reindexed from 1)		H41 L43 K45 R51 C95 S97 L104 F116 S136 H139
Annotation score1
Binding affinityMOAD: ic50=7.5uM
PDBbind-CN: -logKd/Ki=5.12,IC50=7.5uM
BindingDB: IC50=7500nM
Enzymatic activity
Catalytic site (original residue number in PDB) H59 C113 A131 S154 H157
Catalytic site (residue number reindexed from 1) H41 C95 A113 S136 H139
Enzyme Commision number 5.2.1.8: peptidylprolyl isomerase.
Gene Ontology
Molecular Function
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
GO:0003774 cytoskeletal motor activity
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0016859 cis-trans isomerase activity
GO:0031434 mitogen-activated protein kinase kinase binding
GO:0032794 GTPase activating protein binding
GO:0048156 tau protein binding
GO:0050815 phosphoserine residue binding
GO:0050816 phosphothreonine residue binding
GO:0051219 phosphoprotein binding
GO:1990757 ubiquitin ligase activator activity
Biological Process
GO:0000413 protein peptidyl-prolyl isomerization
GO:0001666 response to hypoxia
GO:0001932 regulation of protein phosphorylation
GO:0001934 positive regulation of protein phosphorylation
GO:0007088 regulation of mitotic nuclear division
GO:0010468 regulation of gene expression
GO:0030182 neuron differentiation
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0031647 regulation of protein stability
GO:0032091 negative regulation of protein binding
GO:0032092 positive regulation of protein binding
GO:0032465 regulation of cytokinesis
GO:0042177 negative regulation of protein catabolic process
GO:0043547 positive regulation of GTPase activity
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046785 microtubule polymerization
GO:0050808 synapse organization
GO:0050821 protein stabilization
GO:0060255 regulation of macromolecule metabolic process
GO:0060392 negative regulation of SMAD protein signal transduction
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0080090 regulation of primary metabolic process
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:1900180 regulation of protein localization to nucleus
GO:1902430 negative regulation of amyloid-beta formation
GO:2000146 negative regulation of cell motility
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0030496 midbody
GO:0036064 ciliary basal body
GO:0098978 glutamatergic synapse
GO:0099524 postsynaptic cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kad, PDBe:3kad, PDBj:3kad
PDBsum3kad
PubMed19969456
UniProtQ13526|PIN1_HUMAN Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Gene Name=PIN1)

[Back to BioLiP]