SMTL ID : 6s4a.1

Structure of human MTHFD2 in complex with TH9028

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x KUK: (2~{S})-2-[[5-[[2,4-bis(azanyl)-6-oxidanylidene-5~{H}-pyrimidin-5-yl]carbamoylamino]pyridin-2-yl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid(Non-covalent)

KUK.1: 20 residues within 4Å: Chain A: S.49, Y.50, N.53, K.54, L.96, V.97, Q.98, L.99, D.121, F.123, I.242, R.244, L.255, P.275, G.276, G.279, P.280, T.282, V.283 Ligands: NAD.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.50, A:T.282, A:V.283 Hydrogen bonds: A:S.49, A:N.53, A:K.54, A:V.97, A:Q.98, A:L.99, A:L.99, A:R.244, A:G.276, A:G.279 Water bridges: A:A.141, A:T.142, A:T.142, A:G.277 Salt bridges: A:D.121 pi-Stacking: A:Y.50 pi-Cation interactions: A:K.54 KUK.9: 19 residues within 4Å: Chain B: S.49, Y.50, N.53, K.54, L.96, V.97, Q.98, L.99, D.121, F.123, I.242, L.255, P.275, G.276, G.279, P.280, T.282, V.283 Ligands: NAD.13 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.50, B:T.282, B:V.283 Hydrogen bonds: B:S.49, B:N.53, B:K.54, B:V.97, B:Q.98, B:L.99, B:L.99, B:G.276, B:G.279 Water bridges: B:A.141, B:T.142, B:G.277 Salt bridges: B:D.121 pi-Stacking: B:Y.50 pi-Cation interactions: B:K.54

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

PO4.2: 5 residues within 4Å: Chain A: R.167, R.199 Chain B: D.182, H.185 Ligands: NAD.5 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.167, A:R.199, B:H.185 Hydrogen bonds: B:D.182, B:D.182, B:D.182 Water bridges: B:D.182 PO4.3: 3 residues within 4Å: Chain A: E.43, P.45 Ligands: MPD.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.43 Salt bridges: A:H.48 PO4.4: 2 residues within 4Å: Chain A: V.4, V.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.5 PO4.10: 5 residues within 4Å: Chain A: D.182, H.185 Chain B: R.167, R.199 Ligands: NAD.13 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:D.182, A:D.182, A:H.185 Salt bridges: A:H.185, B:R.167, B:R.199 PO4.11: 3 residues within 4Å: Chain B: E.43, P.45, H.48 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.48 PO4.12: 2 residues within 4Å: Chain B: H.124, V.125 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.124

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

NAD.5: 23 residues within 4Å: Chain A: T.142, A.165, G.166, R.167, S.168, V.171, S.197, H.198, R.199, A.219, A.220, G.221, I.222, L.225, V.240, G.241, I.242, N.243, V.278, G.279, T.282 Ligands: KUK.1, PO4.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.240 Hydrogen bonds: A:R.167, A:S.168, A:R.199, A:R.199, A:A.220, A:I.242, A:N.243, A:V.278, A:T.282 Water bridges: A:S.168, A:R.199 NAD.13: 20 residues within 4Å: Chain B: T.142, G.166, R.167, S.168, V.171, S.197, H.198, R.199, A.219, A.220, G.221, I.222, L.225, V.240, I.242, V.278, G.279, T.282 Ligands: KUK.9, PO4.10 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.142 Hydrogen bonds: B:R.167, B:S.168, B:S.168, B:R.199, B:R.199, B:R.199, B:I.242, B:V.278 Water bridges: B:S.168, B:H.198, B:T.201

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 6 residues within 4Å: Chain A: L.133, D.134, Q.135, H.185, E.186 Chain B: K.169 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.135, A:E.186, B:K.169 Hydrogen bonds: A:D.134, A:E.186 MPD.7: 5 residues within 4Å: Chain A: L.139, W.144, W.147, R.187, P.188 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.144, A:W.147 MPD.8: 3 residues within 4Å: Chain A: H.48, M.69 Ligands: PO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.48 MPD.14: 8 residues within 4Å: Chain B: S.137, M.138, L.139, W.144, N.289, I.292, L.298 Ligands: MPD.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.292, B:L.298 Hydrogen bonds: B:S.137, B:L.139 MPD.15: 4 residues within 4Å: Chain B: E.66, L.82, K.85, L.86 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.85, B:L.86 Hydrogen bonds: B:K.85, B:K.85 MPD.16: 5 residues within 4Å: Chain B: R.20, E.24, A.59, V.60, G.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.59 MPD.17: 8 residues within 4Å: Chain B: L.139, W.144, W.147, E.148, L.178, R.187, P.188 Ligands: MPD.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.144, B:W.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonagas, N. et al., Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress. Nat Cancer (2022)

Release Date

2021-07-07

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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