SMTL ID : 3kjs.1 (1 other biounit)

Crystal Structure of T. cruzi DHFR-TS with 3 high affinity DHFR inhibitors: DQ1 inhibitor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x DQ1: ethyl 4-(5-{[(2,4-diaminoquinazolin-6-yl)methyl]amino}-2-methoxyphenoxy)butanoate(Non-covalent)

DQ1.1: 19 residues within 4Å: Chain A: V.26, V.27, A.28, I.41, W.43, N.44, V.45, D.48, M.49, F.52, T.80, I.84, P.85, F.88, L.91, I.154, Y.160, T.178 Ligands: NAP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.41, A:I.84, A:L.91 Hydrogen bonds: A:V.27, A:S.83, A:Y.160, A:T.178 Water bridges: A:I.41 Salt bridges: A:D.48 pi-Stacking: A:F.52, A:F.52 DQ1.10: 18 residues within 4Å: Chain B: V.26, V.27, A.28, I.41, W.43, N.44, V.45, D.48, M.49, F.52, T.80, I.84, P.85, L.91, I.154, Y.160, T.178 Ligands: NAP.12 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.41, B:I.84, B:L.91 Hydrogen bonds: B:V.26, B:T.178, B:T.178 Water bridges: B:S.83, B:S.83 Salt bridges: B:D.48 pi-Stacking: B:F.52, B:F.52

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

NAP.2: 27 residues within 4Å: Chain A: V.27, A.28, I.35, G.36, D.37, G.38, R.39, S.40, I.41, G.77, R.78, K.79, T.80, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: DQ1.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.41, A:T.80 Hydrogen bonds: A:A.28, A:I.35, A:D.37, A:D.37, A:G.38, A:R.39, A:S.40, A:G.77, A:R.78, A:K.79, A:T.80, A:T.80, A:S.101, A:T.102, A:G.156, A:G.157, A:S.158, A:S.158, A:V.159, A:Y.160 Salt bridges: A:R.78 NAP.12: 27 residues within 4Å: Chain B: V.27, A.28, I.35, G.36, D.37, G.38, R.39, S.40, I.41, G.77, R.78, K.79, T.80, L.99, S.100, S.101, T.102, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: DQ1.10 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.41, B:T.80 Hydrogen bonds: B:A.28, B:I.35, B:D.37, B:D.37, B:G.38, B:G.38, B:R.39, B:G.77, B:R.78, B:K.79, B:T.80, B:T.80, B:S.101, B:G.156, B:G.157, B:S.158, B:S.158, B:V.159, B:Y.160 Water bridges: B:S.83 Salt bridges: B:R.78, B:K.79

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.233, R.235 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.233, A:R.235 SO4.8: 5 residues within 4Å: Chain A: R.257, R.423, S.424 Chain B: R.383, R.384 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.424 Water bridges: A:R.257, A:R.257 Salt bridges: A:R.423, B:R.383, B:R.384 SO4.9: 4 residues within 4Å: Chain A: R.383, R.384 Chain B: R.423, S.424 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.424 Salt bridges: B:R.423, A:R.383, A:R.384 Water bridges: A:R.383 SO4.11: 2 residues within 4Å: Chain B: R.233, R.235 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.233, B:R.235

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

EDO.4: 3 residues within 4Å: Chain A: R.286, W.289, Y.509 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.286 Water bridges: A:W.289, A:R.290 EDO.5: 5 residues within 4Å: Chain A: I.211, S.212, E.213, E.214, Y.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.212, A:E.214, A:E.214 EDO.6: 6 residues within 4Å: Chain A: F.51, Y.176, T.210, F.227, E.228, K.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.210, A:T.210, A:S.212, A:K.229 EDO.7: 3 residues within 4Å: Chain A: I.316, L.429, F.433 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.295, A:N.434 EDO.13: 5 residues within 4Å: Chain B: I.211, S.212, E.213, E.214, Y.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.212, B:E.214, B:E.214 Water bridges: B:E.214 EDO.14: 6 residues within 4Å: Chain B: A.174, Y.176, K.229, I.231, R.482, A.510 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.176, B:K.229 Water bridges: B:Q.173, B:Y.176, B:Y.176, B:K.229, B:A.483 EDO.15: 5 residues within 4Å: Chain B: F.288, G.313, V.314, H.315, I.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.313, B:H.315 EDO.16: 3 residues within 4Å: Chain B: I.316, L.429, F.433 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Synthesis and characterization of potent inhibitors of Trypanosoma cruzi dihydrofolate reductase. Bioorg.Med.Chem. (2010)

Release Date

2010-06-09

Peptides

Dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Dihydrofolate reductase-thymidylate synthase

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