SMTL ID : 4kbn.1 (1 other biounit)

human dihydrofolate reductase complexed with NADPH and 5-{3-[3-(3,5-pyrimidine)]-phenyl-prop-1-yn-1-yl}-6-ethyl-pyrimidine-2,4diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x 25U: 6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine(Non-covalent)

25U.1: 16 residues within 4Å: Chain A: I.7, V.8, A.9, L.22, E.30, F.31, F.34, T.56, I.60, P.61, N.64, L.67, V.115, Y.121, T.136 Ligands: NDP.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.22, A:F.34, A:F.34, A:T.56, A:I.60, A:I.60, A:L.67 Hydrogen bonds: A:I.7, A:Y.121, A:T.136, A:T.136 Salt bridges: A:E.30 pi-Stacking: A:F.31

1 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 5 residues within 4Å: Chain A: V.10, S.11, Q.12, M.14, R.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.11, A:R.137

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: E.171, E.172, K.173, G.174 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: S.42, V.43 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: F.31, Q.35, R.70 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: N.29, R.32 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: P.160, E.161, S.167 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.160, H2O.5 MG.9: 3 residues within 4Å: Chain A: L.166, D.168, Q.170 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: D.168, V.169 No protein-ligand interaction detected (PLIP)

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

NDP.10: 27 residues within 4Å: Chain A: V.8, A.9, I.16, G.17, G.20, D.21, L.22, W.24, G.53, K.54, K.55, T.56, L.75, S.76, R.77, E.78, R.91, V.115, G.116, G.117, S.118, S.119, V.120, Y.121, E.123, T.146 Ligands: 25U.1 27 PLIP interactions: 27 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:S.59, A:S.76, A:R.77, A:E.78, A:G.117, A:S.118, A:S.119 Water bridges: A:L.93, A:L.93, A:S.119, A:E.123, A:T.146, A:T.146, A:T.146 Salt bridges: A:K.54 pi-Cation interactions: A:R.77

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
A

Dihydrofolate reductase

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