SMTL ID : 5sda.1

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-774

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

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

NAP.1: 29 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, 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: GI6.2 30 PLIP interactions: 30 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.19, A:K.55, A:K.55, A:S.119, A:S.120, A:S.120, A:E.124, A:T.147, A:T.147 Salt bridges: A:K.55

1 x GI6: (2R)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanamide(Non-covalent)

GI6.2: 16 residues within 4Å: Chain A: I.8, V.9, A.10, D.22, 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:I.61, A:L.68 Hydrogen bonds: A:I.8, A:D.22, A:Y.122, A:T.137, A:T.137 Water bridges: A:V.9, A:S.60 Salt bridges: A:E.31 pi-Stacking: A:F.32

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

SO4.3: 1 residues within 4Å: Chain A: R.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29 Salt bridges: A:K.174 SO4.4: 4 residues within 4Å: Chain A: R.29, F.32, Q.36, K.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.36 Water bridges: A:R.29 Salt bridges: A:R.29, A:K.69 SO4.5: 2 residues within 4Å: Chain A: R.33, R.37 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.33, A:R.37

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

CL.6: 4 residues within 4Å: Chain A: M.15, R.138, E.151, I.152 Ligand excluded by PLIP

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

EDO.7: 3 residues within 4Å: Chain A: M.38, M.112, Y.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.163 EDO.8: 2 residues within 4Å: Chain A: S.119, F.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.119, A:F.148 Water bridges: A:S.119

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-774. to be published

Release Date

2022-02-09

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

Related Entries With Identical Sequence