SMTL ID : 4gae.1

Crystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: G.22, T.24, G.25, S.26, I.27, Y.51, V.52, N.53, K.54, S.55, H.74, G.118, I.119, D.120, Q.123, A.141, N.142, K.143, E.144, D.169, W.234, M.236, G.237, I.240, M.298 Ligands: FOB.2, FOQ.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.27, A:I.240 Hydrogen bonds: A:G.22, A:T.24, A:T.24, A:T.24, A:G.25, A:S.26, A:S.26, A:S.26, A:I.27, A:N.53, A:K.54, A:S.55, A:S.55, A:H.74, A:I.119, A:D.120, A:D.120, A:S.121, A:Q.123, A:N.142, A:K.143, A:E.144, A:G.237 Water bridges: A:G.28, A:N.53, A:N.53 NDP.8: 27 residues within 4Å: Chain B: G.22, T.24, G.25, S.26, I.27, Y.51, V.52, N.53, K.54, S.55, H.74, G.118, I.119, D.120, Q.123, A.141, N.142, K.143, E.144, D.169, W.234, M.236, G.237, I.240, M.298 Ligands: FOB.9, FOQ.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.27 Hydrogen bonds: B:G.22, B:T.24, B:T.24, B:T.24, B:G.25, B:S.26, B:S.26, B:S.26, B:I.27, B:N.53, B:K.54, B:S.55, B:S.55, B:I.119, B:D.120, B:N.142, B:K.143, B:G.237 Water bridges: B:G.28 pi-Stacking: B:Y.51

2 x FOB: [(1R)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid(Non-covalent)

FOB.2: 16 residues within 4Å: Chain A: D.169, S.170, E.171, S.207, S.208, W.234, M.236, I.240, S.244, N.249, K.250, E.253, C.276 Ligands: NDP.1, FOQ.3, MN.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.234 Hydrogen bonds: A:D.169, A:S.170, A:S.208, A:G.209, A:G.210, A:N.249, A:K.250, A:K.250 Water bridges: A:S.207, A:K.250 FOB.9: 19 residues within 4Å: Chain B: K.143, D.169, S.170, E.171, S.207, S.208, G.209, G.210, W.234, M.236, I.240, S.244, N.249, K.250, E.253, C.276 Ligands: NDP.8, FOQ.10, MN.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.234 Hydrogen bonds: B:K.143, B:S.170, B:S.208, B:G.209, B:G.210, B:N.249, B:K.250, B:K.250 Water bridges: B:S.207, B:S.207

2 x FOQ: [(1S)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid(Non-covalent)

FOQ.3: 16 residues within 4Å: Chain A: D.169, S.170, E.171, S.207, S.208, W.234, M.236, I.240, S.244, N.249, K.250, E.253, C.276 Ligands: NDP.1, FOB.2, MN.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.234 Hydrogen bonds: A:D.169, A:D.169, A:S.170, A:S.208, A:N.249, A:K.250, A:K.250 Water bridges: A:S.207, A:G.209, A:G.209, A:K.250 FOQ.10: 17 residues within 4Å: Chain B: K.143, D.169, S.170, E.171, S.207, S.208, W.234, M.236, I.240, S.244, N.249, K.250, E.253, C.276 Ligands: NDP.8, FOB.9, MN.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.234 Hydrogen bonds: B:K.143, B:D.169, B:S.170, B:S.208, B:N.249, B:K.250, B:K.250 Water bridges: B:S.207, B:S.207, B:G.209, B:G.209

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: D.169, S.170, E.171, E.253 Ligands: FOB.2, FOQ.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.169, A:E.171, A:E.171, A:E.253 MN.11: 7 residues within 4Å: Chain B: K.143, D.169, S.170, E.171, E.253 Ligands: FOB.9, FOQ.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.169, B:E.171, B:E.171, B:E.253 MN.12: 3 residues within 4Å: Chain A: D.180 Chain B: Q.177, L.179 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.180, B:Q.177, B:L.179, H2O.2, H2O.5 MN.13: 1 residues within 4Å: Chain B: N.390 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain A: K.183, N.199 Chain B: P.309, R.311 Ligand excluded by PLIP

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

ACT.6: 3 residues within 4Å: Chain A: K.233, Y.295, P.296 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.295 Salt bridges: A:K.233 ACT.14: 2 residues within 4Å: Chain B: Q.392, W.411 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.392 Water bridges: B:N.390, B:N.390

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 1 residues within 4Å: Chain A: D.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.262 EDO.15: 4 residues within 4Å: Chain B: P.338, S.379, S.380, S.383 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.379, B:S.383 EDO.16: 2 residues within 4Å: Chain B: P.309, D.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, J. et al., Antimalarial and Structural Studies of Pyridine-containing Inhibitors of 1-Deoxyxylulose-5-phosphate Reductoisomerase. ACS Med Chem Lett (2013)

Release Date

2013-02-06

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast