SMTL ID : 3gn2.1

Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00066730)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX8.2 29 PLIP interactions: 29 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:R.34, A:G.36, A:H.55, A:S.57, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.4: 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: AX8.5 29 PLIP interactions: 29 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: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.6: 28 residues within 4Å: Chain C: 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX8.7 28 PLIP interactions: 28 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:K.33, C:K.33, C:K.33, C:K.33, C:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.8: 28 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: AX8.9, AX8.10 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: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 Water bridges: D:G.36, D:N.113, D:S.115, D:S.227, D:L.228 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

5 x AX8: 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine(Non-covalent)

AX8.2: 14 residues within 4Å: Chain A: F.117, D.181, M.183, C.188, F.191, Y.194, G.225, V.226, W.241, K.244, L.283 Chain D: H.287, A.288 Ligands: NAP.1 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain A pi-Stacking: D:H.287, A:F.117, A:F.191 Halogen bonds: D:A.288, A:W.241 Hydrophobic interactions: A:Y.194, A:V.226 Hydrogen bonds: A:G.225 Water bridges: A:D.181 Salt bridges: A:D.181 AX8.5: 14 residues within 4Å: Chain B: F.117, D.181, M.183, C.188, F.191, Y.194, G.225, V.226, W.241, K.244, L.283 Chain C: H.287, A.288 Ligands: NAP.4 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.194, B:V.226 Hydrogen bonds: B:G.225 Water bridges: B:D.181 Salt bridges: B:D.181 pi-Stacking: B:F.117, B:F.191, C:H.287 Halogen bonds: B:W.241, C:A.288 AX8.7: 14 residues within 4Å: Chain B: H.287, A.288 Chain C: F.117, D.181, M.183, C.188, F.191, Y.194, G.225, V.226, W.241, K.244, L.283 Ligands: NAP.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.191, C:Y.194, C:V.226 Hydrogen bonds: C:G.225 Water bridges: C:C.188, C:Y.194, C:Y.194 Salt bridges: C:D.181 pi-Stacking: C:F.117, C:F.191, B:H.287 Halogen bonds: C:W.241, B:A.288 AX8.9: 15 residues within 4Å: Chain A: H.287, A.288 Chain D: F.117, D.181, M.183, C.188, F.191, Y.194, G.225, V.226, W.241, K.244, L.283 Ligands: NAP.8, AX8.10 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.194, D:V.226, D:L.283 Hydrogen bonds: D:G.225 Salt bridges: D:D.181 pi-Stacking: D:F.117, D:F.191, A:H.287 Halogen bonds: D:W.241, A:A.288 AX8.10: 8 residues within 4Å: Chain D: R.34, F.117, Y.194, G.225, P.230, M.233 Ligands: NAP.8, AX8.9 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.230 Water bridges: D:F.117 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 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

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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