Structure of PDB 6ic5 Chain A Binding Site BS01

Receptor Information

>6ic5 Chain A (length=118) Species: 9606 (Homo sapiens)

DTPANCTYLDLLGTWVFQVGSSGSQRDVNCSVMGPQEKKVVVYLQKLDTA
YDDLGNSGHFTIIYNQGFEIVLNDYKWFAFFKYKEEGSKVTTYCNETMTG
WVHDVLGRNWACFTGKKV

Ligand information

• Ligand ID: HB5
• InChI: InChI=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
• InChIKey: IYHCHKSSBYIGIM-JXCXCJIVSA-N
• SMILES:
  CACTVS 3.385: CN1CCN(CC1)[S](=O)(=O)c2ccc(cc2)c3ccc(cc3)[C@H]4C[C@]4(NC(=O)[C@@H](N)Cc5sccc5)C=N
  CACTVS 3.385: CN1CCN(CC1)[S](=O)(=O)c2ccc(cc2)c3ccc(cc3)[CH]4C[C]4(NC(=O)[CH](N)Cc5sccc5)C=N
  OpenEye OEToolkits 2.0.6: CN1CCN(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
• Formula: C28 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
• PDB chain: 6ic5 Chain B Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ic5 Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D1 P3
• Binding residue (residue number reindexed from 1): D1 P3
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.22,IC50=6nM

Enzymatic activity

• Enzyme Commision number: 3.4.14.1: dipeptidyl-peptidase I.

External links

• PDB: RCSB:6ic5, PDBe:6ic5, PDBj:6ic5
• PDBsum: 6ic5
• PubMed: 30978322
• UniProt: P53634|CATC_HUMAN Dipeptidyl peptidase 1 (Gene Name=CTSC)