SMTL ID : 5uy8.1 (1 other biounit)

Crystal structure of AICARFT bound to an antifolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x 8UM: 5-[(5S)-5-ethyl-5-methyl-6-oxo-1,4,5,6-tetrahydropyridin-3-yl]-N-(6-fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)thiophene-2-sulfonamide(Non-covalent)

8UM.1: 19 residues within 4Å: Chain A: K.275, M.321, S.322, F.324, G.325, D.348, K.367, N.498 Chain B: N.440, Q.458, S.459, R.460, I.461, F.550, P.552, F.553, D.555, N.556 Ligands: AMZ.6 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.461, B:F.550, B:P.552, B:F.553, A:F.324, A:F.324 Hydrogen bonds: B:N.440, B:R.460, B:I.461, B:D.555, B:N.556, A:K.275, A:K.275, A:D.348, A:K.367 Halogen bonds: A:S.322 8UM.5: 19 residues within 4Å: Chain A: N.440, Q.458, S.459, R.460, I.461, F.550, P.552, F.553, D.555, N.556 Chain B: K.275, M.321, S.322, F.324, G.325, D.348, K.367, N.498 Ligands: AMZ.2 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.461, A:F.550, A:P.552, A:F.553, B:F.324 Hydrogen bonds: A:N.440, A:R.460, A:I.461, A:D.555, A:N.556, B:K.275, B:K.275, B:D.348, B:K.367 Halogen bonds: B:S.322

3 x AMZ: AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE(Non-covalent)

AMZ.2: 15 residues within 4Å: Chain A: N.440, R.460, A.549, F.550, R.597, F.599 Chain B: R.216, Y.217, I.247, N.248, K.275, H.276, G.325, D.348 Ligands: 8UM.5 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Y.217, B:N.248, B:H.276, B:D.348, B:D.348, A:N.440, A:R.460, A:F.550 Water bridges: B:R.216, B:I.247, B:N.248, A:R.597, A:R.597 Salt bridges: B:R.216, A:R.597 pi-Stacking: A:F.599 AMZ.3: 21 residues within 4Å: Chain A: S.19, V.20, S.21, K.23, S.43, G.44, G.45, T.46, G.72, R.73, V.74, K.75, T.76, L.77, C.110, N.111, L.112, Y.113, D.134, G.136, G.137 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.43, A:S.43, A:G.45, A:T.46, A:G.72, A:R.73, A:K.75, A:K.75, A:T.76, A:L.77, A:N.111, A:Y.113, A:D.134, A:G.136 Salt bridges: A:K.23, A:K.75 AMZ.6: 15 residues within 4Å: Chain A: R.216, Y.217, I.247, N.248, K.275, H.276, G.325, D.348 Chain B: N.440, R.460, A.549, F.550, R.597, F.599 Ligands: 8UM.1 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:N.440, B:R.460, B:F.550, A:Y.217, A:N.248, A:H.276, A:D.348, A:D.348 Water bridges: B:R.597, A:R.216, A:I.247, A:N.248 Salt bridges: B:R.597, A:R.216 pi-Stacking: B:F.599

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: V.434, T.437, S.439, S.441, D.548, L.598, H.600 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.434, A:T.437, A:D.548, A:L.598 MG.7: 7 residues within 4Å: Chain B: V.434, T.437, S.439, S.441, D.548, L.598, H.600 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.434, B:T.437, B:D.548, B:L.598

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fales, K.R. et al., Discovery of N-(6-Fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)-5-[(3R)-3-hydroxypyrrolidin-1-yl]thiophene-2-sulfonamide (LSN 3213128), a Potent and Selective Nonclassical Antifolate Aminoimidazole-4-carboxamide Ribonucleotide Formyltransferase (AICARFT) Inhibitor Effective at Tumor Suppression in a Cancer Xenograft Model. J. Med. Chem. (2017)

Release Date

2018-01-10

Peptides

Bifunctional purine biosynthesis protein PURH: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional purine biosynthesis protein PURH

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