SMTL ID : 9isl.1

Human MTHFD1 in complex with compound 16e

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

4 x 01: (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-chloranyl-phenyl]carbonylamino]pentanedioic acid

01.1: 16 residues within 4Å: Chain A: Y.52, V.55, K.56, V.99, Q.100, L.101, D.125, L.127, I.176, I.238, P.272, G.273, G.276, P.277, V.280 Ligands: NAP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.280 Hydrogen bonds: A:K.56, A:V.99, A:Q.100, A:L.101, A:L.101, A:G.273, A:G.276 Water bridges: A:G.276, A:G.276 Salt bridges: A:D.125 pi-Stacking: A:Y.52 01.3: 16 residues within 4Å: Chain B: Y.52, V.55, K.56, L.98, V.99, Q.100, L.101, D.125, L.127, I.238, P.272, G.273, G.276, P.277, V.280 Ligands: NAP.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.55, B:V.280 Hydrogen bonds: B:K.56, B:V.99, B:Q.100, B:L.101, B:L.101, B:G.273 Water bridges: B:G.274, B:G.276 Salt bridges: B:D.125 pi-Stacking: B:Y.52 01.5: 16 residues within 4Å: Chain C: Y.52, V.55, K.56, L.98, V.99, Q.100, L.101, D.125, L.127, I.238, P.272, G.273, G.276, P.277, V.280 Ligands: NAP.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.55, C:V.280 Hydrogen bonds: C:K.56, C:V.99, C:Q.100, C:L.101, C:L.101, C:G.273, C:G.276 Water bridges: C:G.274, C:G.276 Salt bridges: C:D.125 pi-Stacking: C:Y.52 01.7: 16 residues within 4Å: Chain D: Y.52, V.55, K.56, V.99, Q.100, L.101, D.125, L.127, I.176, I.238, P.272, G.273, G.276, P.277, V.280 Ligands: NAP.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.55, D:V.280 Hydrogen bonds: D:K.56, D:V.99, D:Q.100, D:L.101, D:L.101, D:G.273 Water bridges: D:V.99, D:G.276, D:G.276 Salt bridges: D:D.125 pi-Stacking: D:Y.52

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

NAP.2: 22 residues within 4Å: Chain A: T.148, V.171, G.172, R.173, S.174, V.177, H.196, S.197, L.202, A.215, T.216, G.217, Q.218, M.221, C.236, G.237, I.238, D.255, V.275, G.276, T.279 Ligands: 01.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.177 Hydrogen bonds: A:R.173, A:S.174, A:S.174, A:S.197, A:S.197, A:S.197, A:G.217, A:Q.218, A:I.238, A:G.276, A:T.279 Water bridges: A:G.178, A:K.198, A:T.199 Salt bridges: A:R.173 NAP.4: 23 residues within 4Å: Chain B: T.148, V.171, G.172, R.173, S.174, V.177, H.196, S.197, L.202, A.215, T.216, G.217, Q.218, M.221, C.236, G.237, I.238, N.239, D.255, V.275, G.276, T.279 Ligands: 01.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.177 Hydrogen bonds: B:R.173, B:S.197, B:S.197, B:S.197, B:G.217, B:I.238, B:N.239, B:G.276 Water bridges: B:R.173, B:S.174 Salt bridges: B:R.173 NAP.6: 23 residues within 4Å: Chain B: H.201 Chain C: T.148, V.171, G.172, R.173, S.174, V.177, H.196, S.197, L.202, A.215, T.216, G.217, Q.218, M.221, C.236, G.237, I.238, N.239, V.275, G.276, T.279 Ligands: 01.5 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.177 Hydrogen bonds: C:R.173, C:S.174, C:S.174, C:S.197, C:S.197, C:S.197, C:I.238, C:N.239, C:G.276, C:T.279, B:H.201 Water bridges: C:S.174, C:I.176, C:G.178 Salt bridges: C:R.173 NAP.8: 22 residues within 4Å: Chain D: T.148, V.171, G.172, R.173, S.174, I.176, V.177, H.196, S.197, L.202, A.215, T.216, G.217, Q.218, M.221, C.236, G.237, I.238, V.275, G.276, T.279 Ligands: 01.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.177 Hydrogen bonds: D:R.173, D:S.174, D:S.174, D:S.197, D:S.197, D:S.197, D:I.238, D:N.239 Water bridges: D:G.178 Salt bridges: D:R.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, H.H. et al., Development of Potent and Selective Inhibitors of Methylenetetrahydrofolate Dehydrogenase 2 for Targeting Acute Myeloid Leukemia: SAR, Structural Insights, and Biological Characterization. J.Med.Chem. (2024)

Release Date

2025-01-01

Peptides

C-1-tetrahydrofolate synthase, cytoplasmic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

C-1-tetrahydrofolate synthase, cytoplasmic