SMTL ID : 6jid.1

Human MTHFD2 in complex with Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x BQC: 5-(4-oxo-2-phenyl-1,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6(4H)-carbonyl)-1,3-dihydro-2H-2lambda~6~,1-benzothiazole-2,2-dione(Non-covalent)

BQC.1: 11 residues within 4Å: Chain A: Y.69, N.72, K.73, Q.117, L.118, I.261, P.294, G.295, G.298, P.299, V.302 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.69, A:Y.69, A:I.261, A:V.302 Hydrogen bonds: A:N.72, A:K.73, A:Q.117, A:G.295 pi-Stacking: A:Y.69 BQC.5: 12 residues within 4Å: Chain B: Y.69, N.72, K.73, Q.117, L.118, P.119, P.294, G.295, G.298, P.299, V.302 Ligands: GOL.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.69, B:V.302 Hydrogen bonds: B:N.72, B:K.73, B:Q.117, B:G.295, B:G.296 pi-Stacking: B:Y.69

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

PO4.2: 4 residues within 4Å: Chain A: R.186, R.218 Chain B: D.201, H.204 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:R.186, A:R.186, A:R.186 Salt bridges: A:R.186, A:R.218, B:H.204 Hydrogen bonds: B:D.201, B:D.201, B:D.201 PO4.6: 4 residues within 4Å: Chain A: D.201, H.204 Chain B: R.186, R.218 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.204, B:R.186, B:R.218

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.156, M.157, L.158, W.163, N.308, I.311, L.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.156, A:L.158, A:N.308 GOL.4: 6 residues within 4Å: Chain A: R.127 Chain B: L.152, D.153, Q.154, H.204, E.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.205 GOL.7: 6 residues within 4Å: Chain B: K.73, D.140, F.142, T.161, T.301 Ligands: BQC.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.73, B:D.140, B:T.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawai, J. et al., Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold. Acs Med.Chem.Lett. (2019)

Release Date

2019-06-05

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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