SMTL ID : 5ke2.1

Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x 6S4: (3~{S})-~{N}-~{tert}-butyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide(Non-covalent)

6S4.1: 7 residues within 4Å: Chain A: W.169, W.174, F.190, D.193, R.195, C.196, E.197 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.169, A:W.169, A:F.190, A:F.190, A:D.193, A:E.197 Hydrogen bonds: A:D.193, A:R.195 pi-Stacking: A:W.169, A:W.174, A:W.174

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: Y.70, S.73, P.127, T.131 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.68 EDO.3: 2 residues within 4Å: Chain A: E.133, R.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.141

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: W.174, K.175, D.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.175 Water bridges: A:D.192 SO4.5: 2 residues within 4Å: Chain A: H.25, K.26 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.26 Water bridges: A:H.25, A:H.25, A:H.25, A:K.26, A:D.46 Salt bridges: A:H.25 SO4.6: 5 residues within 4Å: Chain A: K.40, L.52, L.53, S.54, H.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.54 Water bridges: A:S.54, A:S.54 Salt bridges: A:K.40, A:H.57 SO4.7: 3 residues within 4Å: Chain A: T.117, Q.118, S.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.119, A:S.119 Water bridges: A:Q.118, A:Q.118 SO4.8: 5 residues within 4Å: Chain A: E.168, G.171, T.172, W.173, F.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.171 SO4.9: 2 residues within 4Å: Chain A: R.14, K.26 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.14

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

UNX.10: 2 residues within 4Å: Chain A: H.63, Y.122 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: F.107, G.111, A.113 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: G.111, C.140 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: R.103, T.117 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: K.39, Y.41, R.126 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain A: L.189, R.195, C.196 No protein-ligand interaction detected (PLIP) UNX.16: 4 residues within 4Å: Chain A: I.165, K.166, E.207, P.208 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain A: V.11, I.30 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iqbal, A. et al., Crystal structure of SETDB1 Tudor domain in complex with inhibitor xst06472a. to be published

Release Date

2016-07-13

Peptides

Histone-lysine N-methyltransferase SETDB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETDB1

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