Structure of PDB 1orf Chain A Binding Site BS01

Receptor Information
>1orf Chain A (length=232) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQV
ILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINK
YVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVEITIIDRKV
CNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSF
GLENKCGDPRGPGVYILLSKKHLNWIIMTIKG
Ligand information
Ligand ID0G6
InChIInChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
InChIKeyDVFLYEYCMMLBTQ-VSZNYVQBSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC(CCCNC(=[NH2+])\N)C(O)CCl)C2N(C(=O)C(N)Cc1ccccc1)CCC2
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)N[CH](CCCNC(N)=[NH2+])[CH](O)CCl
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(N)=[NH2+])[C@H](O)CCl
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
OpenEye OEToolkits 1.7.6c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(=[NH2+])N)[C@@H](CCl)O)N
FormulaC21 H34 Cl N6 O3
NameD-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide;
PPACK
ChEMBL
DrugBankDB06841
ZINC
PDB chain1orf Chain A Residue 1 [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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PDB1orf The oligomeric structure of human granzyme A is a determinant of its extended substrate specificity.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H57 R99 D189 S190 C191 G193 S195 S214 F215 G216
Binding residue
(residue number reindexed from 1)		H41 R83 D178 S179 C180 G182 S184 S199 F200 G201
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 N192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H41 D86 N181 G182 D183 S184 G185
Enzyme Commision number 3.4.21.78: granzyme A.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0006955 immune response
GO:0009617 response to bacterium
GO:0031640 killing of cells of another organism
GO:0032078 negative regulation of endodeoxyribonuclease activity
GO:0043065 positive regulation of apoptotic process
GO:0043392 negative regulation of DNA binding
GO:0051354 negative regulation of oxidoreductase activity
GO:0051603 proteolysis involved in protein catabolic process
GO:0051604 protein maturation
GO:0070269 pyroptotic inflammatory response
GO:0140507 granzyme-mediated programmed cell death signaling pathway
GO:1902483 cytotoxic T cell pyroptotic cell death
Cellular Component
GO:0001772 immunological synapse
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1orf, PDBe:1orf, PDBj:1orf
PDBsum1orf
PubMed12819769
UniProtP12544|GRAA_HUMAN Granzyme A (Gene Name=GZMA)

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