Structure of PDB 4nbl Chain A Binding Site BS01

Receptor Information
>4nbl Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDN
LTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGE
GNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQHDVPVI
PDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCE
MLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTK
KLHFFPKS
Ligand information
Ligand ID2J6
InChIInChI=1S/C16H13FN4O/c17-12-5-4-11(14(22)9-12)10-21-16-13(3-1-6-18-16)15-19-7-2-8-20-15/h1-9,22H,10H2,(H,18,21)
InChIKeyYTVDOVJPKJLMHL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Oc1cc(F)ccc1CNc2ncccc2c3ncccn3
ACDLabs 12.01Fc1ccc(c(O)c1)CNc2ncccc2c3ncccn3
OpenEye OEToolkits 1.7.6c1cc(c(nc1)NCc2ccc(cc2O)F)c3ncccn3
FormulaC16 H13 F N4 O
Name5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol
ChEMBLCHEMBL3613794
DrugBank
ZINCZINC000095920687
PDB chain4nbl 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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PDB4nbl Tailoring small molecules for an allosteric site on procaspase-6.
Resolution1.756 Å
Binding residue
(original residue number in PDB)		Y198 T199 L200 P201
Binding residue
(residue number reindexed from 1)		Y164 T165 L166 P167
Annotation score1
Binding affinityMOAD: Kd=0.47uM
PDBbind-CN: -logKd/Ki=6.33,Kd=0.47uM
BindingDB: Kd=470nM
Enzymatic activity
Catalytic site (original residue number in PDB) P62 E63 H121 G122 A163 R164
Catalytic site (residue number reindexed from 1) P39 E40 H98 G99 A140 R141
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
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Cellular Component
External links
PDB RCSB:4nbl, PDBe:4nbl, PDBj:4nbl
PDBsum4nbl
PubMed24259468
UniProtP55212|CASP6_HUMAN Caspase-6 (Gene Name=CASP6)

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