SMTL ID : 6rn7.1

DPP1 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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: 5 residues within 4Å: Chain A: N.5, N.65 Chain C: F.6, L.8 Ligands: DMS.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65 NAG.8: 1 residues within 4Å: Chain B: N.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.47

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

DMS.3: 7 residues within 4Å: Chain A: H.59, F.60, T.61, E.69, V.71 Chain B: Y.75, G.121 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

1 x K9W: (2~{S})-~{N}-[(2~{S})-1-azanyl-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]pyrrolidine-2-carboxamide(Covalent)

K9W.5: 15 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 Chain C: N.10, H.11, A.12 8 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: C:A.12, A:D.1 Hydrogen bonds: C:N.10, B:G.27, B:C.29, B:G.72, B:G.72 Water bridges: B:Q.23

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

CL.6: 6 residues within 4Å: Chain B: F.73, P.74, Y.75, Y.118 Chain C: I.59, V.61 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: K.76, V.105 Chain B: Q.83, S.114, E.115 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.83, B:S.114, A:K.76, A:V.105

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

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