SMTL ID : 6f5s.1

Crystal Structure of KDM4D with tetrazole ligand GF049

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.238, H.244, C.310, C.312 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.238, A:H.244, A:C.310, A:C.312

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

CL.2: 3 residues within 4Å: Chain A: P.113, N.128, K.186 Ligand excluded by PLIP

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

EDO.3: 2 residues within 4Å: Chain A: Q.76, K.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.76, A:K.91, A:K.91 EDO.4: 3 residues within 4Å: Chain A: H.115, N.117, F.118 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.118 EDO.5: 3 residues within 4Å: Chain A: F.118, I.264, T.265 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.265, A:T.265 Water bridges: A:K.50, A:T.211, A:T.265 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: F.28, N.29, D.30, F.31, Q.151, W.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.31, A:K.150, A:W.152 Water bridges: A:D.30, A:D.32

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

SO4.8: 3 residues within 4Å: Chain A: R.102, H.103, N.106 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.106 Water bridges: A:H.103, A:H.103, A:H.103, A:H.103 Salt bridges: A:R.102, A:H.103 SO4.9: 5 residues within 4Å: Chain A: D.64, N.65, I.66, S.67, R.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.65, A:S.67, A:S.67 Salt bridges: A:R.102 SO4.10: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.128, A:N.128 Salt bridges: A:R.123, A:K.124, A:K.127

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

NI.11: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: CQT.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.3

1 x CQT: ~{N}-(3-morpholin-4-ylpropyl)-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide(Non-covalent)

CQT.12: 13 residues within 4Å: Chain A: D.139, Y.179, Y.181, F.189, H.192, E.194, D.195, K.210, W.212, K.245, H.280, T.318 Ligands: NI.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.189, A:F.189 Hydrogen bonds: A:Y.181, A:N.202, A:K.210, A:K.210 Water bridges: A:K.245, A:K.245, A:N.294, A:N.294 Salt bridges: A:D.139, A:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazole ligand GF049. 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

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