Structure of PDB 2nqg Chain A Binding Site BS03

Receptor Information

>2nqg Chain A (length=322) Species: 10116 (Rattus norvegicus)

NAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYG
IKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILH
RVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQ
GNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPS
DLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQV
TYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDG
EFWMSFRDFIREFTKLEICNLT

Ligand information

• Ligand ID: NQG
• InChI: InChI=1S/C28H39N9O7/c1-2-44-23(39)14-22(38)27(43)36-19(9-5-11-29)25(41)35-20(10-6-12-33-28(31)32)26(42)37-21(24(30)40)13-16-15-34-18-8-4-3-7-17(16)18/h3-4,7-8,15,19-22,34,38H,2,5-6,9-10,12-14H2,1H3,(H2,30,40)(H,35,41)(H,36,43)(H,37,42)(H4,31,32,33)/t19-,20-,21-,22-/m0/s1
• InChIKey: QRCIRXHNWBRPBN-CMOCDZPBSA-N
• SMILES:
  ACDLabs 10.04: O=C(OCC)CC(O)C(=O)NC(C(=O)NC(C(=O)NC(C(=O)N)Cc2c1ccccc1nc2)CCCNC(=[N@H])N)CCC#N
  OpenEye OEToolkits 1.5.0: [H]/N=C(/N)\NCCC[C@@H](C(=O)N[C@@H](Cc1c[nH]c2c1cccc2)C(=O)N)NC(=O)[C@H](CCC#N)NC(=O)[C@H](CC(=O)OCC)O
  CACTVS 3.341: CCOC(=O)C[CH](O)C(=O)N[CH](CCC#N)C(=O)N[CH](CCCNC(N)=N)C(=O)N[CH](Cc1c[nH]c2ccccc12)C(N)=O
  CACTVS 3.341: CCOC(=O)C[C@H](O)C(=O)N[C@@H](CCC#N)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O
  OpenEye OEToolkits 1.5.0: [H]N=C(N)NCCCC(C(=O)NC(Cc1c[nH]c2c1cccc2)C(=O)N)NC(=O)C(CCC#N)NC(=O)C(CC(=O)OCC)O
• Formula: C28 H39 N9 O7
• Name: 5-AZANYLIDYNE-N-[(2S)-4-ETHOXY-2-HYDROXY-4-OXOBUTANOYL]-L-NORVALYL-L-ARGINYL-L-TRYPTOPHANAMIDE
• ZINC: ZINC000016052252
• PDB chain: 2nqg Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2nqg Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): Q109 G113 C115 G208 S251 G271 H272 W298
• Binding residue (residue number reindexed from 1): Q77 G81 C83 G176 S219 G239 H240 W266
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.48,IC50=333nM

Enzymatic activity

• Catalytic site (original residue number in PDB): Q109 C115 H272 N296 W298
• Catalytic site (residue number reindexed from 1): Q77 C83 H240 N264 W266
• Enzyme Commision number: 3.4.22.52: calpain-1.

Gene Ontology

Molecular Function

• GO:0004198 calcium-dependent cysteine-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2nqg, PDBe:2nqg, PDBj:2nqg
• PDBsum: 2nqg
• PubMed: 17218315
• UniProt: P97571|CAN1_RAT Calpain-1 catalytic subunit (Gene Name=Capn1)