SMTL ID : 3inv.1

Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH NADPH, dUMP AND C-448 ANTIFOLATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-dimer

Ligands

2 x C50: 1-[3-(2,3-dichlorophenoxy)propoxy]-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine(Non-covalent)

C50.1: 17 residues within 4Å: Chain A: V.26, V.27, A.28, I.41, D.48, M.49, F.52, T.80, S.83, I.84, P.85, F.88, L.91, I.154, Y.160, T.178 Ligands: NDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.28, A:I.41, A:F.52, A:T.80 Hydrogen bonds: A:V.26, A:V.27, A:T.178 Salt bridges: A:D.48 C50.6: 18 residues within 4Å: Chain B: V.26, V.27, A.28, I.41, D.48, M.49, F.52, R.53, T.80, S.83, I.84, P.85, F.88, L.91, I.154, Y.160, T.178 Ligands: NDP.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.28, B:I.41, B:F.52, B:T.80 Hydrogen bonds: B:V.26, B:T.178, B:T.178 Salt bridges: B:D.48 Halogen bonds: B:R.53

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

NDP.2: 29 residues within 4Å: Chain A: V.27, A.28, I.35, G.36, D.37, G.38, R.39, S.40, I.41, W.43, 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, V.189 Ligands: C50.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.80, A:Y.160 Hydrogen bonds: A:A.28, A:I.35, A:D.37, A:G.38, A:G.38, A:R.39, A:G.77, A:R.78, A:R.78, A:K.79, A:T.80, A:S.101, A:T.102, A:G.155, A:G.157, A:S.158, A:S.158, A:S.158, A:V.159, A:Y.160 Water bridges: A:I.41 Salt bridges: A:R.78 NDP.7: 28 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, V.189 Ligands: C50.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.80 Hydrogen bonds: B:A.28, B:I.35, B:G.38, B:G.38, B:R.39, B:G.77, B:G.77, B:R.78, B:K.79, B:T.80, B:T.80, B:S.101, B:T.102, 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

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.3: 16 residues within 4Å: Chain A: R.257, C.403, H.404, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 Chain B: R.383, R.384 Ligands: GOL.4, GOL.5 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.257, A:Q.422, A:S.424, A:D.426, A:N.434, A:N.434, A:H.464 Water bridges: A:P.401, A:R.423, B:R.383 Salt bridges: A:R.423, B:R.383, B:R.384 UMP.8: 16 residues within 4Å: Chain A: R.383, R.384 Chain B: C.403, H.404, Q.422, R.423, S.424, C.425, D.426, G.430, V.431, N.434, H.464, Y.466 Ligands: GOL.10, GOL.11 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.422, B:S.424, B:D.426, B:V.431, B:N.434, B:N.434, B:H.464, B:Y.466 Salt bridges: B:R.423, A:R.383, A:R.384 Water bridges: A:R.384, A:R.384

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.429, G.430, F.433 Ligands: UMP.3, GOL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.429 GOL.5: 9 residues within 4Å: Chain A: E.295, F.299, W.317, Y.343, H.404, F.433, N.434 Ligands: UMP.3, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.343 GOL.9: 4 residues within 4Å: Chain A: G.267 Chain B: Q.239, Q.269, R.271 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.239, B:Q.269, B:R.271 Water bridges: B:Q.269, B:R.271, A:Q.269 GOL.10: 4 residues within 4Å: Chain B: I.316, G.430 Ligands: UMP.8, GOL.11 No protein-ligand interaction detected (PLIP) GOL.11: 10 residues within 4Å: Chain B: E.295, F.299, I.316, W.317, Y.343, H.404, F.433, N.434 Ligands: UMP.8, GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.434 Water bridges: B:H.404, B:S.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chitnumsub, P. et al., Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase. To be Published

Release Date

2010-07-28

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase

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