SMTL ID : 6h10.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 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: 4 residues within 4Å: Chain A: P.113, N.128, W.185, K.186 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: F.261, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.261, A:N.262

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

EDO.4: 4 residues within 4Å: Chain A: R.123, K.124, K.127, N.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:K.124, A:K.127, A:N.128 EDO.5: 6 residues within 4Å: Chain A: K.150, Q.151, W.152, N.153, H.156, L.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.29, A:N.153, A:N.153 Water bridges: A:W.152, A:W.152 EDO.6: 5 residues within 4Å: Chain A: P.251, T.252, K.255, R.263 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.251, A:R.263, A:R.263 EDO.7: 2 residues within 4Å: Chain A: C.168, K.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305, A:K.305 EDO.8: 5 residues within 4Å: Chain A: E.122, R.123, W.126, P.251 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.123, A:T.252, A:T.252 EDO.9: 6 residues within 4Å: Chain A: F.118, E.122, T.211, R.263, I.264, T.265 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.264, A:T.265 Water bridges: A:T.265, A:T.265, A:T.265 EDO.10: 4 residues within 4Å: Chain A: E.27, K.33, Y.34, Y.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.27 Water bridges: A:K.33 EDO.11: 7 residues within 4Å: Chain A: Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: FJ8.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.181, A:N.294 Water bridges: A:S.200, A:N.202 EDO.12: 2 residues within 4Å: Chain A: Q.116, N.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.116, A:N.117

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

SO4.13: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62, A:N.65 Water bridges: A:R.60, A:R.60, A:R.60, A:T.62 Salt bridges: A:R.60

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

NI.14: 4 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: FJ8.15 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.10

2 x FJ8: ~{N}-[(~{E})-(4-methylphenyl)methylideneamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanamide(Non-covalent)

FJ8.15: 11 residues within 4Å: Chain A: Y.136, F.189, H.192, E.194, S.200, N.202, K.210, W.212, H.280 Ligands: EDO.11, NI.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.189, A:W.212 Hydrogen bonds: A:Y.136, A:Y.136, A:S.200, A:S.200 FJ8.16: 11 residues within 4Å: Chain A: Y.63, R.102, A.105, N.106, Q.111, T.112, L.206, G.207, E.208, G.286, F.287 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.63, A:L.206, A:E.208, A:F.287, A:F.287 Hydrogen bonds: A:N.106, A:T.112, A:E.208, A:F.287 Water bridges: A:R.102, A:T.112, A:T.112

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.17: 5 residues within 4Å: Chain A: M.19, I.20, F.21, Y.37, Q.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.20, A:I.20 Water bridges: A:Y.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073. To be published

Release Date

2020-01-29

Peptides

Lysine-specific demethylase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4D

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