SMTL ID : 6kg2.1

Human MTHFD2 in complex with Compound 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x D8C: N-[2-chloranyl-4-[[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxidanylidene-2,4-dihydro-1H-chromeno[3,4-c]pyridin-3-yl]carbonyl]phenyl]methanesulfonamide(Non-covalent)

D8C.1: 14 residues within 4Å: Chain A: R.28, Y.69, N.72, K.73, Q.117, L.118, I.261, L.274, P.294, G.295, G.298, P.299, V.302 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.261, A:V.302 Hydrogen bonds: A:R.28, A:N.72, A:Q.117, A:G.295, A:G.298 Water bridges: A:G.296 Salt bridges: A:K.73 pi-Stacking: A:Y.69 D8C.4: 12 residues within 4Å: Chain B: Y.69, N.72, K.73, Q.117, L.118, I.261, P.294, G.295, G.298, P.299, V.302 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.69, B:V.302 Hydrogen bonds: B:N.72, B:Q.117, B:G.295, B:G.296 Water bridges: B:G.298 Salt bridges: B:K.73 pi-Stacking: B:Y.69

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 24 residues within 4Å: Chain A: T.161, A.184, G.185, R.186, S.187, N.189, V.190, S.216, H.217, R.218, A.238, A.239, G.240, I.241, L.244, V.259, G.260, I.261, N.262, V.297, G.298, T.301 Ligands: D8C.1, PO4.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.161, A:V.190 Hydrogen bonds: A:G.185, A:R.186, A:S.187, A:S.187, A:N.189, A:R.218, A:R.218, A:V.259, A:I.261, A:N.262, A:T.301 Water bridges: A:S.187, A:G.191 NAD.5: 23 residues within 4Å: Chain B: T.161, A.184, G.185, R.186, S.187, N.189, V.190, H.217, R.218, A.238, A.239, G.240, I.241, L.244, V.259, G.260, I.261, N.262, V.297, G.298, T.301 Ligands: D8C.4, PO4.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.161, B:V.190 Hydrogen bonds: B:R.186, B:S.187, B:S.187, B:N.189, B:R.218, B:R.218, B:V.259, B:I.261, B:N.262 Water bridges: B:G.191, B:G.191

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

PO4.3: 5 residues within 4Å: Chain A: R.186, R.218 Chain B: D.201, H.204 Ligands: NAD.2 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.186, B:D.201, B:D.201, B:D.201 Salt bridges: A:R.186, A:R.218, B:H.204 Water bridges: B:D.201 PO4.6: 5 residues within 4Å: Chain A: D.201, H.204 Chain B: R.186, R.218 Ligands: NAD.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.186, B:R.218, A:H.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawai, J. et al., Discovery of a Potent, Selective, and Orally Available MTHFD2 Inhibitor (DS18561882) with in Vivo Antitumor Activity. J.Med.Chem. (2019)

Release Date

2019-11-13

Peptides

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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