Structure of PDB 6ic5 Chain B Binding Site BS01

Receptor Information
>6ic5 Chain B (length=162) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HLPTSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRILTNNSQ
TPILSPQEVVSCSQYAQGCEGGFPYLIAGKYAQDFGLVEEACFPYTGTDS
PCKMKEDCFRYYSSEYHYVGGFYGGCNEALMKLELVHHGPMAVAFEVYDD
FLHYKKGIYHHT
Ligand information
Ligand IDHB5
InChIInChI=1S/C28H33N5O3S2/c1-32-12-14-33(15-13-32)38(35,36)24-10-8-21(9-11-24)20-4-6-22(7-5-20)25-18-28(25,19-29)31-27(34)26(30)17-23-3-2-16-37-23/h2-11,16,19,25-26,29H,12-15,17-18,30H2,1H3,(H,31,34)/b29-19+/t25-,26+,28+/m1/s1
InChIKeyIYHCHKSSBYIGIM-JXCXCJIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CC1)[S](=O)(=O)c2ccc(cc2)c3ccc(cc3)[C@H]4C[C@]4(NC(=O)[C@@H](N)Cc5sccc5)C=N
CACTVS 3.385CN1CCN(CC1)[S](=O)(=O)c2ccc(cc2)c3ccc(cc3)[CH]4C[C]4(NC(=O)[CH](N)Cc5sccc5)C=N
OpenEye OEToolkits 2.0.6CN1CCN(CC1)S(=O)(=O)c2ccc(cc2)c3ccc(cc3)C4CC4(C=N)NC(=O)C(Cc5cccs5)N
OpenEye OEToolkits 2.0.6[H]/N=C/[C@]1(C[C@@H]1c2ccc(cc2)c3ccc(cc3)S(=O)(=O)N4CCN(CC4)C)NC(=O)[C@H](Cc5cccs5)N
FormulaC28 H33 N5 O3 S2
Name(2~{S})-2-azanyl-~{N}-[(1~{R},2~{R})-1-(iminomethyl)-2-[4-[4-(4-methylpiperazin-1-yl)sulfonylphenyl]phenyl]cyclopropyl]-3-thiophen-2-yl-propanamide
ChEMBL
DrugBank
ZINC
PDB chain6ic5 Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ic5 Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G232 C234 E275 G276 G277 F278 A349
Binding residue
(residue number reindexed from 1)		G27 C29 E70 G71 G72 F73 A144
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.22,IC50=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q228 C234
Catalytic site (residue number reindexed from 1) Q23 C29
Enzyme Commision number 3.4.14.1: dipeptidyl-peptidase I.
Gene Ontology
Molecular Function
GO:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:6ic5, PDBe:6ic5, PDBj:6ic5
PDBsum6ic5
PubMed30978322
UniProtP53634|CATC_HUMAN Dipeptidyl peptidase 1 (Gene Name=CTSC)

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