SMTL ID : 6ic5.1

Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: Y.93, N.95, E.96, K.116 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.93 NAG-NAG-BMA-MAN-MAN.6: 4 residues within 4Å: Chain D: Y.93, N.95, E.96, K.116 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.93 NAG-NAG-BMA-MAN-MAN.11: 4 residues within 4Å: Chain G: Y.93, N.95, E.96, K.116 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.93 Hydrogen bonds: G:Y.93 NAG-NAG-BMA-MAN-MAN.16: 4 residues within 4Å: Chain J: Y.93, N.95, E.96, K.116 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:Y.93 Hydrogen bonds: J:Y.93

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: N.5 Chain C: F.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.5, A:N.5, A:N.5 NAG.3: 6 residues within 4Å: Chain B: N.47 Chain D: D.53, L.54 Chain K: H.1, L.2, T.4 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain K Hydrophobic interactions: D:L.54, K:T.4 Hydrogen bonds: B:N.47 NAG.7: 2 residues within 4Å: Chain D: N.5 Chain F: F.6 3 PLIP interactions: 3 interactions with chain D Water bridges: D:N.5, D:N.5, D:N.5 NAG.8: 6 residues within 4Å: Chain A: D.53, L.54 Chain E: N.47 Chain H: H.1, L.2, T.4 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H, 1 interactions with chain A Hydrogen bonds: E:N.47 Hydrophobic interactions: H:T.4, A:L.54 NAG.12: 2 residues within 4Å: Chain G: N.5 Chain I: F.6 3 PLIP interactions: 3 interactions with chain G Water bridges: G:N.5, G:N.5, G:N.5 NAG.13: 6 residues within 4Å: Chain E: H.1, L.2, T.4 Chain H: N.47 Chain J: D.53, L.54 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain J, 1 interactions with chain E Hydrogen bonds: H:N.47 Hydrophobic interactions: J:L.54, E:T.4 NAG.17: 2 residues within 4Å: Chain J: N.5 Chain L: F.6 3 PLIP interactions: 3 interactions with chain J Water bridges: J:N.5, J:N.5, J:N.5 NAG.18: 6 residues within 4Å: Chain B: H.1, L.2, T.4 Chain G: D.53, L.54 Chain K: N.47 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain K, 1 interactions with chain G Hydrophobic interactions: B:T.4, G:L.54 Hydrogen bonds: K:N.47

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain B: F.73, P.74, Y.75, Y.118 Chain C: V.61 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain E: F.73, P.74, Y.75, Y.118 Chain F: V.61 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain H: F.73, P.74, Y.75, Y.118 Chain I: V.61 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain K: F.73, P.74, Y.75, Y.118 Chain L: V.61 Ligand excluded by PLIP

4 x HB5: (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(Covalent)

HB5.5: 19 residues within 4Å: Chain A: D.1, T.2, P.3 Chain B: Q.23, G.27, S.28, C.29, Y.30, E.70, G.71, G.72, F.73, P.74, A.144 Chain C: T.9, N.10, H.11, A.12, I.59 10 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: C:I.59, A:D.1, B:F.73, B:A.144 Hydrogen bonds: C:N.10, A:D.1, B:Q.23, B:C.29, B:G.72 Water bridges: B:C.26 HB5.10: 19 residues within 4Å: Chain D: D.1, T.2, P.3 Chain E: Q.23, G.27, S.28, C.29, Y.30, E.70, G.71, G.72, F.73, P.74, A.144 Chain F: T.9, N.10, H.11, A.12, I.59 10 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: F:I.59, E:F.73, E:A.144, D:D.1 Hydrogen bonds: F:N.10, E:Q.23, E:C.29, E:G.72, D:D.1 Water bridges: E:C.26 HB5.15: 19 residues within 4Å: Chain G: D.1, T.2, P.3 Chain H: Q.23, G.27, S.28, C.29, Y.30, E.70, G.71, G.72, F.73, P.74, A.144 Chain I: T.9, N.10, H.11, A.12, I.59 10 PLIP interactions: 6 interactions with chain H, 2 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: H:F.73, H:A.144, I:I.59, G:D.1 Hydrogen bonds: H:Q.23, H:C.29, H:G.72, I:N.10, G:D.1 Water bridges: H:C.26 HB5.20: 19 residues within 4Å: Chain J: D.1, T.2, P.3 Chain K: Q.23, G.27, S.28, C.29, Y.30, E.70, G.71, G.72, F.73, P.74, A.144 Chain L: T.9, N.10, H.11, A.12, I.59 10 PLIP interactions: 6 interactions with chain K, 2 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: K:F.73, K:A.144, L:I.59, J:D.1 Hydrogen bonds: K:Q.23, K:C.29, K:G.72, L:N.10, J:D.1 Water bridges: K:C.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korkmaz, B. et al., Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C. Biochem. Pharmacol. (2019)

Release Date

2019-04-24

Peptides

Dipeptidyl peptidase 1: ADGJ
Dipeptidyl peptidase 1: BEHK
Dipeptidyl peptidase 1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
C

F
C

I
C

L
C

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

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