Structure of PDB 4nbn Chain A Binding Site BS01

Receptor Information
>4nbn Chain A (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNL
TRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEG
NHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQHDVPVIP
DTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEM
LGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKK
LHFFPKS
Ligand information
Ligand ID2J7
InChIInChI=1S/C18H18N4O2/c23-15-7-3-1-5-13(15)10-19-17-9-18(22-12-21-17)20-11-14-6-2-4-8-16(14)24/h1-9,12,23-24H,10-11H2,(H2,19,20,21,22)
InChIKeyXTLGIBKGPXLOFA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(c(c1)CNc2cc(ncn2)NCc3ccccc3O)O
CACTVS 3.385Oc1ccccc1CNc2cc(NCc3ccccc3O)ncn2
ACDLabs 12.01n2c(NCc1ccccc1O)cc(nc2)NCc3ccccc3O
FormulaC18 H18 N4 O2
Name2,2'-[pyrimidine-4,6-diylbis(iminomethanediyl)]diphenol
ChEMBL
DrugBank
ZINCZINC000095920814
PDB chain4nbn Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nbn Tailoring small molecules for an allosteric site on procaspase-6.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		V197 Y198 T199 L200 P201 E214
Binding residue
(residue number reindexed from 1)		V162 Y163 T164 L165 P166 E179
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.36,Kd=44uM
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
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Cellular Component
External links
PDB RCSB:4nbn, PDBe:4nbn, PDBj:4nbn
PDBsum4nbn
PubMed24259468
UniProtP55212|CASP6_HUMAN Caspase-6 (Gene Name=CASP6)

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