SMTL ID : 6rx0.1

Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 3 (NMT-C0013)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: G.30, K.33, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: KM5.3 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:N.56, A:N.56, A:S.57, A:D.82, A:L.83, A:T.84, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:Y.194, A:K.198, A:S.227, A:L.228 Water bridges: A:A.32, A:K.33, A:R.34, A:G.36, A:H.55, A:H.55, A:S.57, A:S.57, A:N.113, A:S.115 Salt bridges: A:K.33, A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.5: 27 residues within 4Å: Chain B: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: KM5.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, B:H.55, B:H.55, B:N.56, B:N.56, B:S.57, B:D.82, B:D.82, B:L.83, B:T.84, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:Y.194, B:K.198, B:S.227, B:L.228 Water bridges: B:G.36, B:S.57, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 NAP.7: 22 residues within 4Å: Chain C: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, Y.194, K.198, P.224, G.225 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:S.57, C:D.82, C:L.83, C:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:K.198 Water bridges: C:G.36, C:N.113, C:N.113, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.8: 27 residues within 4Å: Chain D: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: KM5.9 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, D:N.56, D:N.56, D:S.57, D:D.82, D:D.82, D:L.83, D:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:L.228 Water bridges: D:R.34, D:G.36, D:S.57, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

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

ACT.2: 3 residues within 4Å: Chain A: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34 Salt bridges: A:R.37

3 x KM5: methyl 1-[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-ethyl-amino]phenyl]carbonylpiperidine-4-carboxylate(Non-covalent)

KM5.3: 16 residues within 4Å: Chain A: R.34, S.115, F.117, P.119, D.181, F.191, Y.194, G.225, V.226, L.228, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.191, A:V.226, A:P.230, A:W.241, A:W.241 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:Y.194 pi-Stacking: A:F.117, A:F.117 KM5.6: 13 residues within 4Å: Chain B: R.34, S.115, F.117, P.119, D.181, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.226, B:P.230, B:W.241, B:W.241 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117, B:F.117 KM5.9: 15 residues within 4Å: Chain D: R.34, S.115, F.117, Y.118, P.119, D.181, F.191, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.191, D:V.226, D:P.230, D:W.241, D:W.241 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194 Water bridges: D:Y.194, D:Y.194 pi-Stacking: D:F.117, D:F.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.235, K.238, R.242 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.235, A:K.238, A:R.242, A:R.242 Water bridges: A:E.235, A:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pohner, I. et al., Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1. J.Med.Chem. (2022)

Release Date

2020-07-15

Peptides

Pteridine reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase

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