SMTL ID : 6vsg.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(trifluoromethyl)benzene-1,2-diamine(fragment 17)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: T.110, H.159 Chain B: I.36, H.40, E.92 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.159, B:H.40, H2O.5, H2O.5, H2O.5, H2O.7 CO.2: 3 residues within 4Å: Chain A: I.36, H.40, E.92 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.1, H2O.1, H2O.5, H2O.6

1 x X0V: 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE(Non-covalent)

X0V.3: 7 residues within 4Å: Chain A: I.22, F.33, T.48, L.52, L.59, I.96 Ligands: NAP.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.33, A:L.52

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: A.9, I.22, W.24, R.25, L.26, D.29, Q.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.26, A:D.29, A:Q.30

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

NAP.5: 27 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: X0V.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:R.18, A:G.20, A:G.20, A:D.21, A:G.45, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:R.69, A:R.69, A:Q.70, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102, A:Y.102 Water bridges: A:G.17, A:S.51, A:R.69, A:R.69, A:L.84 Salt bridges: A:R.46, A:R.47 NAP.6: 26 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:I.16, B:R.18, B:G.20, B:G.20, B:R.46, B:R.46, B:R.47, B:R.47, B:T.48, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Water bridges: B:G.17, B:S.51, B:R.69 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Acs Infect Dis. (2020)

Release Date

2020-07-15

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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