SMTL ID : 3gn1.1

Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00067116)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: 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: AX7.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, 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:G.30, A:G.36, A:S.57, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.4: 26 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 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, 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.30, B:A.32, B:G.36, B:H.55, B:H.55, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.5: 27 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, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX7.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.34, C:I.35, C:H.55, C:N.56, C:N.56, 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, C:S.227, C:L.228 Water bridges: C:A.32, C:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 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: AX7.9 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, 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:G.36, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

3 x AX7: 1H-BENZIMIDAZOL-2-AMINE(Non-covalent)

AX7.2: 5 residues within 4Å: Chain A: F.117, D.181, Y.194, V.226 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.117, A:V.226 Hydrogen bonds: A:Y.194, A:Y.194 Salt bridges: A:D.181 pi-Stacking: A:F.117 pi-Cation interactions: A:F.117 AX7.6: 6 residues within 4Å: Chain C: F.117, D.181, Y.194, V.226, P.230 Ligands: NAP.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.226, C:P.230 Hydrogen bonds: C:Y.194, C:Y.194 Salt bridges: C:D.181 pi-Stacking: C:F.117 pi-Cation interactions: C:F.117 AX7.9: 6 residues within 4Å: Chain D: F.117, D.181, Y.194, V.226, P.230 Ligands: NAP.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.226 Hydrogen bonds: D:Y.194, D:Y.194, D:Y.194 Salt bridges: D:D.181 pi-Stacking: D:F.117 pi-Cation interactions: D:F.117

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

ACT.3: 3 residues within 4Å: Chain A: K.33, R.34, R.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34 Water bridges: A:R.37 Salt bridges: A:R.37 ACT.7: 2 residues within 4Å: Chain C: V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78 Water bridges: C:N.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpamhanga, C.P. et al., One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening. J.Med.Chem. (2009)

Release Date

2009-12-29

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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