SMTL ID : 6h0w.1

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS035

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 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 NA: SODIUM ION(Non-functional Binders)

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

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

EDO.3: 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.4: 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.5: 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.6: 6 residues within 4Å: Chain A: K.109, Q.111, P.113, N.132, W.185, K.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.111, A:N.132 Water bridges: A:Q.111 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.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.123 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 EDO.11: 8 residues within 4Å: Chain A: Y.181, E.194, S.200, A.292, I.293, N.294 Ligands: FHW.15, I1L.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.181, A:S.200, A:S.200, A:N.294 Water bridges: A:Y.181

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

SO4.12: 4 residues within 4Å: Chain A: R.60, E.61, T.62, N.65 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.61, A:T.62, A:T.62 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.13: 5 residues within 4Å: Chain A: H.192, E.194, H.280 Ligands: FHW.15, I1L.17 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.192, A:E.194, A:H.280, H2O.6

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

CL.14: 4 residues within 4Å: Chain A: P.113, N.128, W.185, K.186 Ligand excluded by PLIP

1 x FHW: (2~{R})-3-phenyl-2-(2~{H}-1,2,3,4-tetrazol-5-yl)propanehydrazide(Non-covalent)

FHW.15: 14 residues within 4Å: Chain A: Y.136, Y.181, F.189, H.192, E.194, N.202, K.210, W.212, K.245, H.280, A.290 Ligands: EDO.11, NI.13, I1L.17 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.189, A:N.202, A:W.212, A:A.290 Hydrogen bonds: A:Y.136, A:E.194, A:K.245 Water bridges: A:Y.181, A:A.190, A:A.190 pi-Stacking: A:Y.181 pi-Cation interactions: A:K.210

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

EPE.16: 2 residues within 4Å: Chain A: K.255, E.256 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.256 Salt bridges: A:K.255

1 x I1L: [2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoylamino]azanium(Non-covalent)

I1L.17: 13 residues within 4Å: Chain A: Y.136, Y.181, F.189, H.192, E.194, S.200, N.202, K.210, W.212, H.280 Ligands: EDO.11, NI.13, FHW.15 9 PLIP interactions: 9 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, A:N.202 Water bridges: A:K.210, A:N.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malecki, P.H. et al., Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS035. 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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