SMTL ID : 4kak.2 (1 other biounit)

Crystal structure of human dihydrofolate reductase complexed with NADPH and 6-ethyl-5-[(3S)-3-[3-methoxy-5-(pyridine-4-yl)phenyl]but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP1006)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NDP.1: 28 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, V.115, G.117, S.118, S.119, V.120, Y.121, E.123, T.146 Ligands: 06U.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:A.9, A:I.16, 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.59, A:S.76, A:R.77, A:E.78, A:E.78, A:G.117, A:S.118, A:S.118, A:S.119, A:Y.121, A:T.146 Water bridges: A:S.119, A:T.146 Salt bridges: A:K.54

1 x 06U: 6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine(Non-covalent)

06U.2: 17 residues within 4Å: Chain A: I.7, V.8, A.9, D.21, E.30, F.31, F.34, T.56, S.59, I.60, P.61, N.64, L.67, V.115, Y.121, T.136 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.31, A:F.34, A:F.34, A:T.56, A:I.60, A:L.67 Hydrogen bonds: A:I.7, A:T.136, A:T.136 Salt bridges: A:E.30 pi-Stacking: A:F.31, A:F.34

2 x EOH: ETHANOL(Non-functional Binders)

EOH.3: 2 residues within 4Å: Chain A: P.61, E.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.62 EOH.4: 1 residues within 4Å: Chain A: K.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.157

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: R.32, Q.35, R.36 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.32, H2O.4, H2O.5, H2O.6 CA.6: 5 residues within 4Å: Chain A: V.10, S.11, Q.12, R.137, I.138 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.138, H2O.1, H2O.4 CA.7: 3 residues within 4Å: Chain A: K.132, Y.162, E.183 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.183, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lamb, K.M. et al., Elucidating features that drive the design of selective antifolates using crystal structures of human dihydrofolate reductase. Biochemistry (2013)

Release Date

2013-10-09

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydrofolate reductase

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