SMTL ID : 6f5r.1

Crystal Structure of KDM4D with GF028 ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.228, H.234, C.300, S.301, C.302 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.228, A:H.234, A:C.300, A:C.302

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: P.103, N.118, K.176 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: R.113, K.114, K.117, N.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.113, A:R.113, A:K.117, A:N.118 EDO.4: 6 residues within 4Å: Chain A: K.140, Q.141, W.142, N.143, H.146, L.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.143, A:N.143 Water bridges: A:N.19, A:W.142, A:W.142 EDO.5: 4 residues within 4Å: Chain A: P.241, T.242, K.245, R.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.253, A:R.253 EDO.6: 2 residues within 4Å: Chain A: C.158, K.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.295, A:K.295 EDO.7: 7 residues within 4Å: Chain A: F.108, E.112, T.201, R.253, I.254, T.255 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.108, A:T.255 EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: Y.171, E.184, N.192, A.282 Ligands: CQZ.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.192 EDO.10: 3 residues within 4Å: Chain A: E.17, Y.24, Y.27 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: R.253, I.254, T.255 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.253, A:T.255, A:T.255

1 x NI: NICKEL (II) ION(Non-covalent)

NI.12: 4 residues within 4Å: Chain A: H.182, E.184, H.270 Ligands: CQZ.15 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.182, A:E.184, A:H.270, H2O.1, H2O.5

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

SO4.13: 5 residues within 4Å: Chain A: D.54, N.55, I.56, S.57, R.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.55, A:S.57, A:S.57 Salt bridges: A:R.92 SO4.14: 3 residues within 4Å: Chain A: R.92, H.93, N.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.96 Water bridges: A:H.93, A:H.93 Salt bridges: A:H.93

1 x CQZ: 2-(3-oxidanylpropylamino)pyridine-4-carboxylic acid(Non-covalent)

CQZ.15: 10 residues within 4Å: Chain A: Y.126, F.179, A.180, H.182, K.200, W.202, K.235, H.270 Ligands: EDO.9, NI.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.179, A:W.202, A:K.235 Hydrogen bonds: A:Q.78, A:Y.126, A:A.180 Water bridges: A:N.192 Salt bridges: A:K.200 pi-Stacking: A:F.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with GF028 ligand. To be published

Release Date

2018-12-12

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D