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SMTL ID : 8v92.1

BRD4 BD1 liganded with macrocyclic compound 2b (JJ-II-352A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x 01: (4bS)-1-ethyl-21-methyl-4b,11,12,22-tetrahydro-2H,10H,18H-dibenzo[13',14':6',7'][1,5,9]trioxacyclotetradecino[12',11':4,5]pyrido[2,3-d]pyrimidine-2,4,20(1H,3H)-trione

01.1:

16 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, K.50, L.51, N.52, L.53, Y.56, Y.98, N.99, D.104, I.105, M.108
Ligands: EDO.3

8 PLIP interactions:

8 interactions with chain A

Hydrophobic interactions: A:W.40, A:P.41, A:F.42, A:L.51, A:I.105
Hydrogen bonds: A:N.99, A:N.99
Water bridges: A:P.41

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

EDO.2:	7 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, T.90, N.94, I.97 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:N.94 Water bridges: A:T.62, A:T.62
EDO.3:	7 residues within 4Å: Chain A: W.40, P.41, Q.44, K.50, L.51 Ligands: 01.1, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50
EDO.4:	3 residues within 4Å: Chain A: W.40, K.50 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.40
EDO.5:	5 residues within 4Å: Chain A: N.89, F.92, T.93, Y.96, E.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.113 Water bridges: A:Y.96, A:E.113, A:E.113
EDO.6:	9 residues within 4Å: Chain A: P.6, T.9, Q.43, Q.44, P.45, D.65, G.67, T.68, K.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.71
EDO.7:	2 residues within 4Å: Chain A: R.17, Q.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18 Water bridges: A:R.17, A:Q.18
EDO.8:	4 residues within 4Å: Chain A: Q.21, L.123, T.125, E.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:E.126 Water bridges: A:Q.21
EDO.9:	1 residues within 4Å: Chain A: K.61 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Schonbrunn, E. et al., Macrocyclic dihydropyridine inhibitors of BET bromodomains. To be published

Release Date

2025-03-19

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Bromodomain-containing protein 4

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2oss.1 | 2yel.1 | 3mxf.1 | 3p5o.1 | 3svf.1 | 3svg.1 | 3u5j.1 | 3u5k.1 | 3u5k.2 | 3u5k.3 | 3u5k.4 | 3u5l.1 | 3uvw.1 | 3uvx.1 | 3uvy.1 | 3uw9.1 | 3uw9.2 | 3zyu.1 | 3zyu.2 | 4a9l.1 | 4bw1.1 | 4bw2.1 | 4bw3.1 | 4bw4.1 | 4c67.1 | 4cfk.1 | 4cfl.1 | 4cl9.1 | 4clb.1 | 4e96.1 more...less...

4f3i.1 | 4gpj.1 | 4hbv.1 | 4hbx.1 | 4hby.1 | 4ioo.1 | 4ioq.1 | 4ior.1 | 4j0r.1 | 4j0s.1 | 4j3i.1 | 4lyi.1 | 4lzs.1 | 4men.1 | 4meo.1 | 4mep.1 | 4meq.1 | 4mr3.1 | 4mr4.1 | 4nqm.1 | 4nr8.1 | 4nuc.1 | 4nud.1 | 4nue.1 | 4o70.1 | 4o70.2 | 4o71.1 | 4o71.2 | 4o72.1 | 4o74.1 | 4o74.2 | 4o75.1 | 4o76.1 | 4o76.2 | 4o76.3 | 4o76.4 | 4o77.1 | 4o77.2 | 4o78.1 | 4o7a.1 | 4o7b.1 | 4o7c.1 | 4o7e.1 | 4o7e.2 | 4o7f.1 | 4o7f.2 | 4ogi.1 | 4ogi.2 | 4ogj.1 | 4ogj.2 | 4pce.1 | 4pci.1 | 4ps5.1 | 4ps5.2 | 4qb3.1 | 4qzs.1 | 4uiy.1 | 4uiz.1 | 4whw.1 | 4wiv.1 | 4xy9.1 | 4xya.1 | 4zc9.1 | 5a85.1 | 5acy.1 | 5acy.2 | 5ad2.1 | 5ad2.2 | 5ad3.1 | 5ad3.2 | 5bt4.1 | 5bt4.2 | 5bt4.3 | 5cfw.1 | 5d26.1 | 5d3l.1 | 5d3p.1 | 5d3r.1 | 5d3t.1 | 5dlx.1 | 5dlz.1 | 5e0r.1 | 5egu.1 | 5egu.2 | 5egu.3 | 5egu.4 | 5ei4.1 | 5eis.1 | 5f5z.1 | 5f60.1 | 5f61.1 | 5f61.2 | 5f62.1 | 5f63.1 | 5fbx.1 | 5hcl.1 | 5hq5.1 | 5igk.1 | 5kdh.1 | 5khm.1 | 5kj0.1 | 5lj1.1 | 5lj2.1 | 5luu.1 | 5m39.1 | 5m39.2 | 5m3a.1 | 5mkz.1 | 5mli.1 | 5n2m.1 | 5nnc.1 | 5nnc.2 | 5nnd.1 | 5nnd.2 | 5nne.1 | 5nnf.1 | 5nng.1 | 5o97.1 | 5ovb.1 | 5ovb.2 | 5owm.1 | 5oww.1 | 5oww.2 | 5oww.3 | 5oww.4 | 5ti2.1 | 5ti3.1 | 5ti4.1 | 5ti5.1 | 5ti6.1 | 5ti7.1 | 5ula.1 | 5ula.2 | 5v67.1 | 5vbo.1 | 5vbp.1 | 5vbp.2 | 5wma.1 | 5you.1 | 5yov.1 | 5z8g.1 | 5z8r.1 | 5z8z.1 | 5z90.1 | 5z9k.1 | 6afr.1 | 6bn7.1 | 6bn9.1 | 6bnb.1 | 6boy.1 | 6cd5.1 | 6ciy.1 | 6dmj.1 | 6dml.1 | 6fnx.1 | 6fo5.1 | 6fsy.1 | 6ft3.1 | 6ft4.1 | 6g0d.1 | 6g0e.1 | 6g0f.1 | 6g0g.1 | 6g0h.1 | 6g0o.1 | 6g0p.1 | 6g0q.1 | 6g0r.1 | 6g0s.1 | 6hdq.1 | 6hov.1 | 6i7x.1 | 6i7y.1 | 6ked.1 | 6kee.1 | 6kef.1 | 6keg.1 | 6mh1.1 | 6mh1.2 | 6mh7.1 | 6mh7.2 | 6q3y.1 | 6q3y.2 | 6q3z.1 | 6q3z.2 | 6rwj.1 | 6s25.1 | 6s4b.1 | 6s6k.1 | 6sa2.1 | 6sa3.1 | 6sah.1 | 6saj.1 | 6sb8.1 | 6se4.1 | 6swn.1 | 6swq.1 | 6tpx.1 | 6tpy.1 | 6tpz.1 | 6u0d.1 | 6uvj.1 | 6uvm.1 | 6uwu.1 | 6uwx.1 | 6v0u.1 | 6v1k.1 | 6v1l.1 | 6v1u.1 | 6wgx.1 | 6wgx.2 | 6xuz.1 | 6xv3.1 | 6xv3.2 | 6xv3.3 | 6xv3.4 | 6xv7.1 | 6xvc.1 | 6yin.1 | 6yqn.1 | 6yqo.1 | 6yqp.1 | 6yqz.1 | 6z7g.1 | 6z7l.1 | 6z7m.1 | 6zb3.1 | 6zed.1 | 6zel.1 | 6zf9.1 | 7a9u.1 | 7ajn.1 | 7axr.1 | 7b1t.1 | 7k6g.1 | 7k6g.2 | 7k6h.1 | 7l9m.1 | 7lh8.1 | 7m16.1 | 7mlq.1 | 7mlr.1 | 7mls.1 | 7mr5.1 | 7mr6.1 | 7mr7.1 | 7mr8.1 | 7mr9.1 | 7mra.1 | 7mrb.1 | 7o18.1 | 7p6v.1 | 7p6w.1 | 7p6y.1 | 7p6y.2 | 7q3f.1 | 7qdl.1 | 7r5b.1 | 7r9c.1 | 7rel.1 | 7rem.1 | 7rjo.1 | 7rjp.1 | 7rjq.1 | 7rjr.1 | 7rmd.1 | 7rn2.1 | 7rxr.1 | 7rxr.2 | 7rxs.1 | 7rxt.1 | 7ugf.1 | 7uty.1 | 8b96.1 | 8b98.1 | 8bds.1 | 8beb.1 | 8dyr.1 | 8e17.1 | 8e3w.1 | 8ead.1 | 8ewv.1 | 8ewv.2 | 8ewv.3 | 8ewv.4 | 8ewv.5 | 8ewv.6 | 8fvk.1 | 8fvk.2 | 8p9f.1 | 8p9g.1 | 8p9h.1 | 8p9i.1 | 8p9i.2 | 8p9j.1 | 8p9k.1 | 8p9l.1 | 8piq.1 | 8pxa.1 | 8pxm.1 | 8pxm.2 | 8pxn.1 | 8pxn.2 | 8pxn.3 | 8pxn.4 | 8qal.1 | 8qan.1 | 8qap.1 | 8qar.1 | 8v9f.1 | 9f1k.1 | 9f1l.1 | 9f1m.1 | 9f1m.2 | 9f1m.3 | 9f1m.4 | 9f1n.1 | 9f1n.2 | 9f1n.3 | 9f1n.4 | 9fby.1 | 9fwx.1 | 9fxp.1

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