SMTL ID : 7mdn.1

Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-octamer

Ligands

8 x Y6V: ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide(Non-covalent)

Y6V.1: 16 residues within 4Å: Chain A: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, L.108, Q.111 Chain H: D.59, K.107, A.110 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:V.20, A:Y.23, A:Y.23, A:W.26, A:F.56, A:E.62, A:A.64, A:L.108, H:A.110 Hydrogen bonds: A:A.60, A:E.62, A:Q.111 Y6V.3: 16 residues within 4Å: Chain B: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, L.108, Q.111 Chain C: D.59, K.107, A.110 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.20, B:Y.23, B:Y.23, B:W.26, B:F.56, B:E.62, B:A.64, B:L.108, C:A.110 Hydrogen bonds: B:A.60, B:E.62, B:Q.111 Y6V.4: 15 residues within 4Å: Chain C: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, Q.111 Chain D: D.59, K.107, A.110 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:A.110, C:V.20, C:Y.23, C:Y.23, C:W.26, C:F.56, C:E.62, C:A.64 Hydrogen bonds: C:A.60, C:E.62, C:Q.111 Y6V.5: 16 residues within 4Å: Chain D: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, L.108, Q.111 Chain E: D.59, K.107, A.110 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.20, D:Y.23, D:W.26, D:W.26, D:F.56, D:E.62, D:A.64, D:L.108, E:A.110 Hydrogen bonds: D:A.60, D:E.62, D:Q.111 pi-Stacking: D:F.56 Y6V.6: 16 residues within 4Å: Chain B: D.59, K.107, A.110 Chain E: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, L.108, Q.111 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:V.20, E:Y.23, E:Y.23, E:W.26, E:F.56, E:E.62, E:A.64, E:L.108, B:A.110 Hydrogen bonds: E:A.60, E:E.62, E:Q.111 Y6V.8: 16 residues within 4Å: Chain A: D.59, K.107, A.110 Chain F: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, L.108, Q.111 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:V.20, F:Y.23, F:Y.23, F:W.26, F:F.56, F:E.62, F:A.64, F:L.108, A:A.110 Hydrogen bonds: F:A.60, F:E.62, F:Q.111 pi-Stacking: F:F.56 Y6V.9: 15 residues within 4Å: Chain F: D.59, K.107, A.110 Chain G: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, Q.111 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:V.20, G:Y.23, G:Y.23, G:W.26, G:F.56, G:E.62, G:A.64, F:A.110 Hydrogen bonds: G:A.60, G:E.62, G:Q.111 pi-Stacking: G:F.56 Y6V.10: 15 residues within 4Å: Chain G: D.59, K.107, A.110 Chain H: V.20, Y.23, W.26, F.56, F.57, G.58, D.59, A.60, E.62, R.63, A.64, Q.111 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:V.20, H:Y.23, H:Y.23, H:W.26, H:F.56, H:E.62, H:A.64, G:A.110 Hydrogen bonds: H:A.60, H:E.62, H:Q.111

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

UNX.2: 3 residues within 4Å: Chain A: G.106, R.109, A.110 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Chain D: R.63 Chain E: G.58, D.59, Q.118 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dilworth, D. et al., A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization. Nat.Chem.Biol. (2022)

Release Date

2021-05-05

Peptides

Histone-lysine N-methyltransferase NSD2: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Histone-lysine N-methyltransferase NSD2

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