SMTL ID : 6nm4.1 (1 other biounit)

Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.11, C.14, C.22, H.25 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.14, A:C.22, A:H.25

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 11 residues within 4Å: Chain A: A.62, G.63, L.64, G.96, Y.97, R.123, Y.124, V.125, N.126, C.127 Ligands: KS7.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.64, A:Y.97, A:N.126, A:N.126, A:C.127, A:C.127

1 x KS7: 4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane(Non-covalent)

KS7.3: 10 residues within 4Å: Chain A: G.96, S.98, W.99, C.127, A.128, R.129, D.130, W.162, Y.167 Ligands: SAM.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.162, A:W.162 pi-Stacking: A:W.162

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: L.48, L.52, R.53 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allali-Hassani, A. et al., Discovery of a chemical probe for PRDM9. Nat Commun (2019)

Release Date

2019-02-13

Peptides

Histone-lysine N-methyltransferase PRDM9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase PRDM9

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