SMTL ID : 6rn6.1

DPP1 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.5 Chain C: N.4, F.6, L.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.4 NAG.2: 2 residues within 4Å: Chain A: N.95, E.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.96 NAG.4: 3 residues within 4Å: Chain B: N.48 Chain D: D.53, L.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.48

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.76, V.105 Chain B: Q.84, S.115, E.116 Chain D: L.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.84, A:K.76 Water bridges: B:Y.117, A:K.76

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

CL.5: 6 residues within 4Å: Chain B: F.74, P.75, Y.76, Y.119 Chain C: I.59, V.61 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.22, N.23 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: P.4, T.5 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: K.68, L.69 Chain D: Y.75 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain E: F.74, P.75, Y.76, Y.119 Chain F: I.59, V.61 Ligand excluded by PLIP

1 x K9Q: (2~{S},4~{R})-~{N}-[(2~{S})-1-azanyl-3-(4-phenylphenyl)propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide(Covalent)

K9Q.9: 14 residues within 4Å: Chain D: D.1 Chain E: Q.24, G.28, S.29, C.30, Y.31, E.71, G.72, G.73, F.74 Chain F: T.9, N.10, H.11, A.12 7 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:Q.24, E:G.28, E:C.30, E:G.73, D:D.1, F:N.10 Hydrophobic interactions: D:D.1

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: AD
Dipeptidyl peptidase 1: BE
Dipeptidyl peptidase 1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

Dipeptidyl peptidase 1

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