SMTL ID : 4qhv.1

Crystal structure of human dihydrofolate reductase as complex with pyridopyrimidine 22 (N~6~-METHYL-N~6~-[4-(PROPAN-2-YL)PHENYL]PYRIDO[2,3-D]PYRIMIDINE-2,4,6-TRIAMINE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

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

NDP.1: 33 residues within 4Å: Chain A: V.8, A.9, I.16, G.17, K.18, G.20, D.21, L.22, W.24, G.53, K.54, K.55, T.56, S.59, 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: IXF.2, SO4.7, SO4.8 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:A.9, A:G.20, A:G.20, A:G.53, A:K.54, A:K.55, A:K.55, A:T.56, A:T.56, A:S.59, A:R.77, A:E.78, A:E.78, A:L.93, A:G.117, A:S.118, A:S.119, A:Y.121, A:Y.121, A:E.123, A:T.146 Water bridges: A:R.77, A:R.77, A:S.119, A:S.119, A:T.146 Salt bridges: A:K.54, A:K.55, A:K.55

1 x IXF: N~6~-methyl-N~6~-[4-(propan-2-yl)phenyl]pyrido[2,3-d]pyrimidine-2,4,6-triamine(Non-covalent)

IXF.2: 15 residues within 4Å: Chain A: I.7, V.8, A.9, L.22, E.30, F.31, F.34, S.59, P.61, N.64, L.67, V.115, Y.121, T.136 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:N.64, A:L.67 Hydrogen bonds: A:I.7, A:V.8, A:T.136 Water bridges: A:Y.121 Salt bridges: A:E.30 pi-Stacking: A:F.31

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

SO4.3: 4 residues within 4Å: Chain A: V.165, L.166, S.167, D.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:D.168 Water bridges: A:S.167 SO4.4: 2 residues within 4Å: Chain A: E.172, K.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.173 Water bridges: A:E.171, A:G.174 Salt bridges: A:K.173 SO4.5: 5 residues within 4Å: Chain A: L.4, D.94, L.97, H.127, P.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.94, A:H.127 Salt bridges: A:H.127 SO4.6: 4 residues within 4Å: Chain A: I.60, P.61, E.62, R.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.62, A:E.62, A:R.65 SO4.7: 7 residues within 4Å: Chain A: G.53, K.54, K.55, T.56, G.117, V.120 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.53, A:G.53, A:K.54, A:K.55, A:T.56, A:T.56, A:G.117 Water bridges: A:S.119, A:S.119 Salt bridges: A:K.55 SO4.8: 5 residues within 4Å: Chain A: K.54, S.76, R.77, E.78 Ligands: NDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.77, A:E.78 Salt bridges: A:K.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cody, V. et al., Structure-activity correlations for three pyrido[2,3-d]pyrimidine antifolates binding to human and Pneumocystis carinii dihydrofolate reductase. Acta Crystallogr F Struct Biol Commun (2015)

Release Date

2015-06-10

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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