SMTL ID : 3nxt.1

Preferential Selection of Isomer Binding from Chiral Mixtures: Alternate Binding Modes Observed for the E-and Z-isomers of a Series of 5-substituted 2,4-diaminofuro[2m,3-d]pyrimidines as Ternary Complexes with NADPH and Human Dihydrofolate Reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

NDP.1: 30 residues within 4Å: Chain A: V.8, A.9, I.16, G.17, K.18, G.20, D.21, W.24, G.53, K.54, K.55, T.56, L.75, S.76, R.77, E.78, R.91, S.92, L.93, V.115, G.116, G.117, S.118, S.119, V.120, Y.121, E.123, T.146 Ligands: D2E.2, SO4.5 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:A.9, A:K.18, A:G.20, A:G.20, A:G.53, A:G.53, A:K.54, A:K.55, A:T.56, A:T.56, A:S.76, A:R.77, A:R.77, A:E.78, A:L.93, A:G.117, A:S.118, A:Y.121, A:Y.121, A:E.123, A:T.146 Water bridges: A:S.59, A:S.119, A:T.146 Salt bridges: A:K.54

1 x D2E: 5-[(E)-2-cyclopropyl-2-(2-methoxyphenyl)ethenyl]furo[2,3-d]pyrimidine-2,4-diamine(Non-covalent)

D2E.2: 16 residues within 4Å: Chain A: I.7, V.8, A.9, L.22, E.30, F.31, F.34, T.56, S.59, I.60, P.61, L.67, V.115, Y.121, T.136 Ligands: NDP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.34, A:T.56, A:I.60, A:I.60, A:L.67 Hydrogen bonds: A:V.8, A:E.30, A:T.136 Salt bridges: A:E.30 pi-Stacking: A:F.31, A:F.34

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

SO4.3: 4 residues within 4Å: Chain A: V.165, L.166, S.167, D.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.167, A:D.168 SO4.4: 3 residues within 4Å: Chain A: P.61, E.62, R.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.62, A:R.65 SO4.5: 3 residues within 4Å: Chain A: S.118, T.146 Ligands: NDP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.118 Water bridges: A:S.119, A:F.147, A:F.147 SO4.6: 3 residues within 4Å: Chain A: K.122, P.149, E.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.150 Salt bridges: A:K.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cody, V. et al., Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ternary complexes with NADPH and human dihydrofolate reductase. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-12-01

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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