SMTL ID : 6rne.1

DPP1 in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: Y.93, N.95, E.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.93

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

NAG.2: 6 residues within 4Å: Chain A: N.5, N.65 Chain C: F.6, L.8 Ligands: DMS.4, KA8.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.7: 1 residues within 4Å: Chain B: N.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.47

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: H.59, F.60, E.69, V.71 Chain B: Y.75, G.121 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) DMS.4: 7 residues within 4Å: Chain A: N.5, C.6, T.7, N.65 Chain C: N.4, F.6 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.4 pi-Cation interactions: C:F.6 DMS.8: 5 residues within 4Å: Chain B: V.60, S.61, C.62, S.63, Q.64 No protein-ligand interaction detected (PLIP) DMS.9: 4 residues within 4Å: Chain B: Q.23, A.24 Chain C: W.35 Ligands: ACT.12 No protein-ligand interaction detected (PLIP)

1 x KA8: (2~{S},4~{S})-~{N}-[(2~{S})-1-azanyl-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-fluoranyl-pyrrolidine-2-carboxamide(Covalent)

KA8.5: 17 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 Chain C: N.10, H.11, A.12 Ligands: NAG.2 7 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.23, B:G.27, B:C.29, B:G.72, B:G.72, C:N.10 Hydrophobic interactions: A:D.1

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

CL.6: 5 residues within 4Å: Chain B: F.73, P.74, Y.75, Y.118 Chain C: V.61 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 6 residues within 4Å: Chain A: W.101 Chain B: C.62, S.63, Q.64, Y.81, F.85 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.64, B:F.85 Hydrogen bonds: B:Q.64, B:Q.64 ACT.12: 5 residues within 4Å: Chain B: V.147 Chain C: N.10, H.11, W.35 Ligands: DMS.9 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.35, B:V.147 Salt bridges: C:H.11

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 3 residues within 4Å: Chain B: H.117, G.121 Ligands: DMS.3 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.116, B:H.117, B:G.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kack, H. et al., DPP1 Inhibitors: Exploring the Role of Water in the S2 Pocket of DPP1 with Substituted Pyrrolidines. Acs Med.Chem.Lett. (2019)

Release Date

2019-08-28

Peptides

Dipeptidyl peptidase 1: A
Dipeptidyl peptidase 1: B
Dipeptidyl peptidase 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

Related Entries With Identical Sequence