Structure of PDB 6ic6 Chain A Binding Site BS01

Receptor Information

>6ic6 Chain A (length=118) Species: 9606 (Homo sapiens)

DTPANCTYLDLLGTWVFQVGSSGSQRDVNCSVMGPQEKKVVVYLQKLDTA
YDDLGNSGHFTIIYNQGFEIVLNDYKWFAFFKYKEEGSKVTTYCNETMTG
WVHDVLGRNWACFTGKKV

Ligand information

• Ligand ID: H9B
• InChI: InChI=1S/C21H24F3N3O/c1-2-18(26)19(28)27-20(12-25)11-17(20)15-5-3-13(4-6-15)14-7-9-16(10-8-14)21(22,23)24/h3-10,17-18H,2,11-12,25-26H2,1H3,(H,27,28)/t17-,18+,20+/m1/s1
• InChIKey: HMCDKUBGFVFWGK-HBFSDRIKSA-N
• SMILES:
  CACTVS 3.385: CC[CH](N)C(=O)N[C]1(CN)C[CH]1c2ccc(cc2)c3ccc(cc3)C(F)(F)F
  OpenEye OEToolkits 2.0.6: CCC(C(=O)NC1(CC1c2ccc(cc2)c3ccc(cc3)C(F)(F)F)CN)N
  OpenEye OEToolkits 2.0.6: CC[C@@H](C(=O)N[C@@]1(C[C@@H]1c2ccc(cc2)c3ccc(cc3)C(F)(F)F)CN)N
  CACTVS 3.385: CC[C@H](N)C(=O)N[C@]1(CN)C[C@@H]1c2ccc(cc2)c3ccc(cc3)C(F)(F)F
• Formula: C21 H24 F3 N3 O
• Name: (2~{S})-~{N}-[(1~{R},2~{R})-1-(aminomethyl)-2-[4-[4-(trifluoromethyl)phenyl]phenyl]cyclopropyl]-2-azanyl-butanamide
• PDB chain: 6ic6 Chain B Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ic6 Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C.
• Resolution: 1.898 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=7.82,IC50=15nM

Enzymatic activity

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

External links

• PDB: RCSB:6ic6, PDBe:6ic6, PDBj:6ic6
• PDBsum: 6ic6
• PubMed: 30978322
• UniProt: P53634|CATC_HUMAN Dipeptidyl peptidase 1 (Gene Name=CTSC)