SMTL ID : 6dqb.1

LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e. 2-((3-(4-(dimethylamino)but-2-enamido)phenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x H77: 2-{(R)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

H77.1: 20 residues within 4Å: Chain A: R.75, Q.77, Y.151, A.153, D.154, W.212, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, Q.277, L.278, H.313 Ligands: HZV.2, HZM.3, MN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.153, A:D.154, A:W.212, A:W.245 Hydrogen bonds: A:Q.77, A:Y.151, A:C.223 Salt bridges: A:D.154, A:K.243 pi-Stacking: A:F.222

1 x HZV: 2-{(R)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

HZV.2: 21 residues within 4Å: Chain A: R.75, Q.77, R.78, E.81, Y.151, A.153, D.154, W.212, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, L.278, H.313 Ligands: H77.1, HZM.3, MN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.153, A:W.212, A:W.245 Hydrogen bonds: A:Q.77, A:Y.151, A:C.223 Salt bridges: A:E.81, A:D.154, A:K.243 pi-Stacking: A:F.222

1 x HZM: 2-{(S)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid(Non-covalent)

HZM.3: 20 residues within 4Å: Chain A: R.75, Q.77, R.78, E.81, Y.151, A.153, D.154, Y.214, S.221, F.222, C.223, H.225, N.235, K.243, W.245, L.278, H.313 Ligands: H77.1, HZV.2, MN.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.153, A:W.245 Hydrogen bonds: A:Q.77, A:Y.151, A:C.223 Salt bridges: A:E.81, A:K.243 pi-Stacking: A:F.222

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: H77.1, HZV.2, HZM.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.1, H2O.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: E.227, D.228, H.229, W.230, L.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.227, A:H.229 GOL.6: 3 residues within 4Å: Chain A: H.125, M.126, P.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.126

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 8 residues within 4Å: Chain A: L.256, E.257, M.260, R.261, D.273, H.276, Q.277, Y.312 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.273 DMS.8: 2 residues within 4Å: Chain A: S.250, P.309 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J. Med. Chem. (2018)

Release Date

2018-11-21

Peptides

Linked KDM5A Jmj Domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Linked KDM5A Jmj Domain

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