SMTL ID : 6rni.1

DPP1 in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 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: 5 residues within 4Å: Chain A: Y.93, N.95, E.96, K.116, K.117 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.7: 1 residues within 4Å: Chain B: N.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.48

4 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.76, G.122 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 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:F.6 DMS.8: 4 residues within 4Å: Chain B: Q.24, A.25 Chain C: W.35 Ligands: DMS.10 No protein-ligand interaction detected (PLIP) DMS.10: 4 residues within 4Å: Chain B: V.148 Chain C: N.10, H.11 Ligands: DMS.8 No protein-ligand interaction detected (PLIP)

1 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

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

KAQ.6: 19 residues within 4Å: Chain A: D.1, T.2, P.3 Chain B: Q.24, G.28, S.29, C.30, Y.31, E.71, G.72, G.73, F.74, P.75, A.145 Chain C: T.9, N.10, H.11, A.12, I.59 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:G.28, B:C.30, B:G.73, A:D.1, C:N.10 Hydrophobic interactions: A:D.1

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

ACT.9: 6 residues within 4Å: Chain A: W.101 Chain B: C.63, S.64, Q.65, Y.82, F.86 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.65, B:F.86 Hydrogen bonds: B:Q.65, B:Q.65

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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