Structure of PDB 3shf Chain A Binding Site BS01

Receptor Information
>3shf Chain A (length=1133) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDGGITSFVRTVLCEGGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVT
IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQN
LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVL
KAFDNQCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNM
KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFK
RIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC
VLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRS
QLQDLHRKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMASANMHKELC
ALMFSLDWIKAKTELVGPAHLIHEFVAYRHILDEKDCAVCENFQEFLSLN
GHLLGRQPFPNIVQLGLCEPETSEVYRQAKLQAKQEGDTGRLYLEWINKK
TIKNLSRLVVRPHTDAVYHACFSQDGQRIASCGADKTLQVFKAETGEKLL
DIKAHEDEVLCCAFSSDDSYIATCSADKKVKIWDSATGKLVHTYDEHSEQ
VNCCHFTNKSNHLLLATGSNDFFLKLWDLNQKECRNTMFGHTNSVNHCRF
SPDDELLASCSADGTLRLWDVRSANERKSINVKRFFDVEVIVKCCSWSAD
GDKIIVAAKNKVLLFDIHTSGLLAEIHTGHHSTIQYCDFSPYDHLAVIAL
SQYCVELWNIDSRLKVADCRGHLSWVHGVMFSPDGSSFLTASDDQTIRVW
ETKKVCKNSAIVLKQEIDVVFQENETMVLAVDNIRGLQLIAGKTGQIDYL
PEAQVSCCCLSPHLEYVAFGDEDGAIKIIELPNNRVFSSGVGHKKAVRHI
QFTADGKTLISSSEDSVIQVWNWQTGDYVFLQAHQETVKDFRLLQDSRLL
SWSFDGTVKVWNVITGRIERDFTCHQGTVLSCAISSDATKFSSTSADKTA
KIWSFDLLSPLHELKGHNGCVRCSAFSLDGILLATGDDNGEIRIWNVSDG
QLLHSCAPISHGGWVTDVCFSPDSKTLVSAGGYLKWWNVATGDSSQTFYT
NGTNLKKIHVSPDFRTYVTVDNLGILYILQVLE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3shf Chain A Residue 1250 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3shf Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis.
Resolution3.55 Å
Binding residue
(original residue number in PDB)		P123 I125 F126 V127 R129 A156 G157 G159 K160 S161 V162 P321 L322 S325 F425
Binding residue
(residue number reindexed from 1)		P22 I24 F25 V26 R28 A55 G56 G58 K59 S60 V61 P220 L221 S224 F324
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process
GO:0031072 heat shock protein binding
GO:0042802 identical protein binding
GO:0043531 ADP binding
Biological Process
GO:0001666 response to hypoxia
GO:0001822 kidney development
GO:0001843 neural tube closure
GO:0006915 apoptotic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007420 brain development
GO:0007584 response to nutrient
GO:0008635 activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c
GO:0010659 cardiac muscle cell apoptotic process
GO:0030154 cell differentiation
GO:0030900 forebrain development
GO:0042981 regulation of apoptotic process
GO:0051402 neuron apoptotic process
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:0097190 apoptotic signaling pathway
GO:0097193 intrinsic apoptotic signaling pathway
GO:1902510 regulation of apoptotic DNA fragmentation
GO:2001235 positive regulation of apoptotic signaling pathway
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0043293 apoptosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3shf, PDBe:3shf, PDBj:3shf
PDBsum3shf
PubMed21827944
UniProtO88879|APAF_MOUSE Apoptotic protease-activating factor 1 (Gene Name=Apaf1)

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