SMTL ID : 3kvm.1

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid inhibitor 951 at 2.00A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.239, V.241, H.242 4 PLIP interactions: 4 interactions with chain A Water bridges: A:V.241, A:V.241 Salt bridges: A:R.239, A:H.242

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: A.89, A.90, G.91, K.94, G.113, S.114, N.139, Y.141, N.175, N.206, K.249, T.277, N.278, T.279, S.299, G.300, L.303, V.327, G.328, G.329, L.349, Y.350, T.351 Ligands: DOR.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.139, A:Y.141, A:Y.350 Hydrogen bonds: A:A.90, A:K.94, A:S.114, A:S.114, A:N.175, A:K.249, A:K.249, A:N.278, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330, A:V.330, A:V.330

1 x DOR: (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

DOR.3: 13 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, P.210, N.211, N.278, T.279 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.143 Hydrogen bonds: A:N.139, A:N.139, A:G.142, A:F.143, A:N.206, A:N.211, A:N.278, A:N.278, A:T.279 Water bridges: A:S.209 Salt bridges: A:K.94

1 x DET: UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DET.4: 9 residues within 4Å: Chain A: E.47, R.51, H.95, Q.120, R.127, Y.141, N.144, S.145, H.146 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.144 Hydrogen bonds: A:E.47, A:E.47, A:Y.141 Salt bridges: A:E.47

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.305, A:Q.309 Salt bridges: A:R.312

1 x 951: 2-[(2E)-2-{[5-(2-chlorophenyl)furan-2-yl]methylidene}hydrazino]benzoic acid(Non-covalent)

951.6: 18 residues within 4Å: Chain A: Y.32, M.37, L.40, Q.41, P.46, A.49, H.50, A.53, T.57, L.61, L.62, F.92, M.105, V.128, R.130, Y.350, T.354, P.358 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.32, A:P.46, A:H.50, A:A.53, A:F.92, A:V.128, A:Y.350, A:T.354 Hydrogen bonds: A:Q.41 Water bridges: A:T.354 Salt bridges: A:R.130 Halogen bonds: A:T.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLean, L.R. et al., Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-03-02

Peptides

Dihydroorotate dehydrogenase, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase, mitochondrial

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