Structure of PDB 4n5d Chain A Binding Site BS01

Receptor Information
>4n5d 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 ID2FQ
InChIInChI=1S/C9H10N4O/c1-5-11-4-6-3-7(10)9(14)13(2)8(6)12-5/h3-4H,10H2,1-2H3
InChIKeySSAYTTNQRVNWAL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2C(=Cc1c(nc(nc1)C)N2C)N
OpenEye OEToolkits 1.7.6Cc1ncc2c(n1)N(C(=O)C(=C2)N)C
CACTVS 3.385CN1C(=O)C(=Cc2cnc(C)nc12)N
FormulaC9 H10 N4 O
Name6-amino-2,8-dimethylpyrido[2,3-d]pyrimidin-7(8H)-one
ChEMBL
DrugBank
ZINCZINC000098208160
PDB chain4n5d Chain A Residue 401 [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]
PDB4n5d Tailoring small molecules for an allosteric site on procaspase-6.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		N125 Y198 L200
Binding residue
(residue number reindexed from 1)		N101 Y163 L165
Annotation score1
Binding affinityMOAD: Kd=607uM
PDBbind-CN: -logKd/Ki=3.22,Kd=607uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4n5d, PDBe:4n5d, PDBj:4n5d
PDBsum4n5d
PubMed24259468
UniProtP55212|CASP6_HUMAN Caspase-6 (Gene Name=CASP6)

[Back to BioLiP]