Structure of PDB 4nbk Chain A Binding Site BS01

Receptor Information
>4nbk Chain A (length=256) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNL
TRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEG
NHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQHDVPVIP
TNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEML
GKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKL
HFFPKS
Ligand information
Ligand ID2J5
InChIInChI=1S/C13H14N2O/c1-10-5-4-8-14-13(10)15-9-11-6-2-3-7-12(11)16/h2-8,16H,9H2,1H3,(H,14,15)
InChIKeyOIQQRLRYXHZROE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 1.7.6		Cc1cccnc1NCc2ccccc2O
ACDLabs 12.01Oc1c(cccc1)CNc2ncccc2C
FormulaC13 H14 N2 O
Name2-{[(3-methylpyridin-2-yl)amino]methyl}phenol
ChEMBL
DrugBank
ZINCZINC000000394894
PDB chain4nbk Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nbk Tailoring small molecules for an allosteric site on procaspase-6.
Resolution1.936 Å
Binding residue
(original residue number in PDB)		Y198 L200 P201
Binding residue
(residue number reindexed from 1)		Y162 L164 P165
Annotation score1
Binding affinityMOAD: Kd=136uM
PDBbind-CN: -logKd/Ki=3.87,Kd=136uM
Enzymatic activity
Catalytic site (original residue number in PDB) P62 E63 H121 G122 A163 R164
Catalytic site (residue number reindexed from 1) P38 E39 H97 G98 A139 R140
Enzyme Commision number 3.4.22.59: caspase-6.
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004197 cysteine-type endopeptidase activity
GO:0005515 protein binding
GO:0008234 cysteine-type peptidase activity
GO:0042802 identical protein binding
GO:0097153 cysteine-type endopeptidase activity involved in apoptotic process
GO:0097200 cysteine-type endopeptidase activity involved in execution phase of apoptosis
Biological Process
GO:0002218 activation of innate immune response
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0016540 protein autoprocessing
GO:0030855 epithelial cell differentiation
GO:0043065 positive regulation of apoptotic process
GO:0043067 regulation of programmed cell death
GO:0043525 positive regulation of neuron apoptotic process
GO:0051604 protein maturation
GO:0060545 positive regulation of necroptotic process
GO:0070269 pyroptotic inflammatory response
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
GO:0072734 cellular response to staurosporine
GO:0097194 execution phase of apoptosis
GO:0097284 hepatocyte apoptotic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4nbk, PDBe:4nbk, PDBj:4nbk
PDBsum4nbk
PubMed24259468
UniProtP55212|CASP6_HUMAN Caspase-6 (Gene Name=CASP6)

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