SMTL ID : 8cox.1

Mycobacterium tuberculosis dihydrofolate reductase in complex with N-(2-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)methanesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 25 residues within 4Å: Chain A: W.8, A.9, I.16, 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 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.22 Hydrogen bonds: A:A.9, A:I.16, A:R.18, A:G.20, A:G.45, A:R.46, A:R.46, A:R.47, A:R.47, A:R.47, A:T.48, A:R.69, A:R.69, A:R.69, A:Q.70, A:G.97, A:G.98, A:G.99, A:Q.100, A:V.101 Water bridges: A:Y.102 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NDP.6: 26 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, 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: VBJ.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.9, B:I.16, B:G.20, B:G.20, B:G.45, B:R.46, B:R.46, B:R.47, B:R.47, B:R.47, B:T.48, B:T.48, B:S.68, B:R.69, B:G.98, B:G.99, B:Q.100, B:V.101 Salt bridges: B:R.46, B:R.47, B:R.69

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

PO4.2: 2 residues within 4Å: Chain A: R.46, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.46, A:R.47 PO4.3: 1 residues within 4Å: Chain A: R.25 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.25 PO4.7: 1 residues within 4Å: Chain B: R.47 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.47

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

CO.4: 5 residues within 4Å: Chain A: H.159, S.161 Chain B: I.36, H.40, E.92 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.40, A:H.159, H2O.2, H2O.2, H2O.2 CO.5: 3 residues within 4Å: Chain B: T.110, H.159, R.160 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.110

1 x VBJ: ~{N}-[3-[2,6-bis(azanyl)-5-(2-cyclopropylethynyl)pyrimidin-4-yl]phenyl]methanesulfonamide(Non-covalent)

VBJ.8: 13 residues within 4Å: Chain B: I.7, W.8, A.9, I.22, D.29, Q.30, F.33, T.48, L.52, I.96, Y.102, T.115 Ligands: NDP.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.30, B:F.33, B:F.33, B:F.33, B:T.48, B:L.52, B:I.96 Hydrogen bonds: B:W.8, B:Y.102, B:Y.102, B:T.115 Salt bridges: B:D.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkman, T.J. et al., Currently unpublished. To Be Published

Release Date

2024-03-13

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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