SMTL ID : 7w2p.1

Tudor domain of SMN in complex with a small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

1 x 8AI: 2-[(4-fluorophenyl)methyl]-2-azatricyclo[7.3.0.0^{3,7}]dodeca-1(9),3(7)-dien-8-imine(Non-covalent)

8AI.1: 7 residues within 4Å: Chain A: W.21, D.24, Y.28, Y.46, Y.49, N.51 Ligands: UNX.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.21, A:W.21, A:W.21, A:Y.28, A:Y.28, A:Y.28, A:Y.46, A:Y.49, A:Y.49 Hydrogen bonds: A:N.51 pi-Stacking: A:W.21, A:W.21, A:Y.49

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 1 residues within 4Å: Chain A: E.40 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

UNX.4: 1 residues within 4Å: Chain A: N.56 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: T.41, C.42 No protein-ligand interaction detected (PLIP) UNX.6: 5 residues within 4Å: Chain A: I.20, W.21, S.22, E.53, Q.55 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: Y.49 Ligands: 8AI.1 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain A: T.31 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: T.31, V.45, T.47 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: K.12 Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.11: 5 residues within 4Å: Chain A: K.12, V.13, F.37 Ligands: UNX.10, UNX.13 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: N.51, R.52 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain A: K.12, V.13 Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: E.53, E.54 No protein-ligand interaction detected (PLIP) UNX.15: 1 residues within 4Å: Chain A: K.16 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: I.64, C.65, E.66 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II. Nat Commun (2022)

Release Date

2022-10-05

Peptides

Survival motor neuron protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Survival motor neuron protein

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