SMTL ID : 5sd7.1

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-735

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 30 residues within 4Å: Chain A: V.9, A.10, I.17, G.18, K.19, G.21, D.22, L.23, W.25, G.54, K.55, K.56, T.57, S.60, L.76, S.77, R.78, E.79, R.92, S.93, V.116, G.117, G.118, S.119, S.120, V.121, Y.122, E.124, T.147 Ligands: I0E.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.57 Hydrogen bonds: A:A.10, A:I.17, A:K.19, A:G.21, A:G.21, A:G.54, A:G.54, A:K.55, A:K.56, A:T.57, A:S.60, A:S.77, A:R.78, A:R.78, A:E.79, A:G.118, A:S.119, A:S.120, A:T.147 Water bridges: A:K.55, A:K.55, A:E.79, A:E.79, A:S.120, A:S.120, A:E.124, A:T.147 Salt bridges: A:K.55

1 x I0E: (2S)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanoic acid(Non-covalent)

I0E.2: 15 residues within 4Å: Chain A: I.8, V.9, A.10, L.23, E.31, F.32, F.35, S.60, I.61, P.62, L.68, V.116, Y.122, T.137 Ligands: NAP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.23, A:F.32, A:I.61, A:L.68 Hydrogen bonds: A:Y.122, A:Y.122, A:T.137, A:T.137 Water bridges: A:D.22, A:L.23, A:L.23 Salt bridges: A:E.31

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: R.78, R.92 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.78 Salt bridges: A:R.78, A:R.92 PO4.4: 4 residues within 4Å: Chain A: R.29, F.32, Q.36, K.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.36 Water bridges: A:R.29, A:K.69 Salt bridges: A:R.29, A:K.69 PO4.5: 2 residues within 4Å: Chain A: R.33, R.37 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.37 Salt bridges: A:R.33, A:R.37 PO4.6: 3 residues within 4Å: Chain A: Q.48, K.69, G.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48, A:G.70

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

CL.7: 3 residues within 4Å: Chain A: M.15, R.138, I.152 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: K.64, N.65, K.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.64, A:N.65 EDO.9: 5 residues within 4Å: Chain A: G.3, S.4, S.43, D.111, M.112 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.4, A:S.4, A:D.111, A:K.133, A:K.133 Water bridges: A:N.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-735. to be published

Release Date

2022-02-09

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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