7VHZ: EP300 HAT domain

Name: PDB 7VHZ: Crystal structure of EP300 HAT domain in complex with compound 7
Published: 2022-04-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of EP300 HAT domain in complex with compound 7. Determined by X-ray diffraction at 2.0 Å resolution. Released 27 Apr 2022.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,579
Mol. weight: 106.07 kDa
Ligands: 6TI, ZN
Released: 27 Apr 2022

Explore 7VHZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VHZ contains 59 α-helices and 38 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1169-1170	2	1
α-helix	1171-1174	4
β-strand	1175-1176	2	2
β-strand	1184-1185	2	2
β-strand	1190-1194	5	3
β-strand	1198-1201	4	3
α-helix	1202-1206	5
β-strand	1212-1215	4	4
β-strand	1224-1227	4	4
α-helix	1228-1230	3
β-strand	1232-1235	4	3
β-strand	1240-1241	2	1
α-helix	1242-1243	2
β-strand	1244-1246	3	5
β-strand	1253-1255	3	5
α-helix	1256-1259	4
α-helix	1273-1277	5
α-helix	1283-1285	3
α-helix	1294-1295	2
α-helix	1297-1313	17
β-strand	1321-1334	14	6
α-helix	1335-1336	2
α-helix	1337-1339	3
α-helix	1340-1344	5
β-strand	1352-1366	15	6
β-strand	1369-1381	13	6
α-helix	1386	1
β-strand	1392-1400	9	6
α-helix	1407-1409	3
α-helix	1410-1428	19
β-strand	1432-1436	5	6
α-helix	1439-1441	3
α-helix	1455-1459	5
α-helix	1460-1476	17
β-strand	1482-1485	4	6
α-helix	1486-1493	8
α-helix	1498-1500	3
α-helix	1508-1519	12
α-helix	1584-1590	7
α-helix	1592-1594	3
β-strand	1595-1599	5	6
α-helix	1603-1607	5
α-helix	1609-1612	4
α-helix	1617-1618	2
β-strand	1619	1	6
α-helix	1622-1624	3
α-helix	1628-1636	9
α-helix	1644-1663	20

Chain B: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1169	1	7
α-helix	1170-1174	5
β-strand	1175-1176	2	8
β-strand	1184-1185	2	8
β-strand	1190-1194	5	9
β-strand	1198-1201	4	9
α-helix	1202-1206	5
β-strand	1212-1214	3	10
β-strand	1225-1227	3	10
α-helix	1228-1230	3
β-strand	1232-1235	4	9
α-helix	1240	1
β-strand	1241	1	7
α-helix	1242-1243	2
β-strand	1244-1246	3	11
β-strand	1253-1255	3	11
α-helix	1256-1259	4
α-helix	1273-1278	6
α-helix	1283-1285	3
α-helix	1294-1295	2
α-helix	1297-1313	17
β-strand	1321-1334	14	12
α-helix	1335-1336	2
α-helix	1337-1339	3
α-helix	1340-1344	5
β-strand	1352-1366	15	12
β-strand	1369-1381	13	12
α-helix	1386	1
β-strand	1392-1400	9	12
α-helix	1407-1409	3
α-helix	1410-1428	19
β-strand	1432-1436	5	12
α-helix	1439-1441	3
α-helix	1456-1459	4
α-helix	1460-1476	17
β-strand	1482-1485	4	12
α-helix	1486-1492	7
α-helix	1498-1500	3
α-helix	1508-1519	12
α-helix	1584-1590	7
α-helix	1592-1594	3
β-strand	1595-1599	5	12
α-helix	1603-1607	5
α-helix	1609-1612	4
α-helix	1617-1618	2
β-strand	1619	1	12
α-helix	1622-1624	3
α-helix	1628-1636	9
α-helix	1644-1659	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone acetyltransferase p300	A, B	protein	454	Homo sapiens	Q09472 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7VHZ_1 Histone acetyltransferase p300 (chains A, B)
GPSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQNRYHFCEKCFNEIQGESVSLG
DDPSQPQTTINKEQFSKRKNDTLDPELFVECTECGRKMHQICVLHHEIIWPAGFVCDGCL
KKSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVK
PGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYIS
YLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQK
IPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEES
IKESGGSGSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLT
LARDKHLEFSSLRRAQWSTMCMLVELHTQSQDRF

Ligands and cofactors

ID	Name	Formula	Copies
6TI	(2R)-N-(2H-indazol-4-yl)-1-[1-(4-methoxyphenyl)cyclopentyl]carbonyl-pyrrolidine…	C25 H28 N4 O3	2
ZN	Zinc ion	Zn	6

Primary citation

Discovery of EP300/CBP histone acetyltransferase inhibitors through scaffold hopping of 1,4-oxazepane ring. Kanada, R., Kagoshima, Y., Asano, M. et al. Bioorg Med Chem Lett (2022) 66:128726-128726. DOI 10.1016/j.bmcl.2022.128726 · PubMed

Other PDB entries of the same protein (UniProt Q09472 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BT3 1.05 Å, Crystal structure of EP300 bromodomain in complex with SGC-CBP30 chemical probe
3T92 1.5 Å, Crystal structure of the Taz2:C/EBPepsilon-TAD chimera protein
5LPM 1.5 Å, Crystal structure of the bromodomain of human Ep300 bound to the inhibitor XDM3d
5NU5 1.6 Å, Crystal structure of the human bromodomain of EP300 bound to the inhibitor XDM-CBP
3BIY 1.7 Å, Crystal structure of p300 histone acetyltransferase domain in complex with a bisubstrate…
6PGU 1.72 Å, Crystal structure of the p300 acetyltransferase domain with allosteric inhibitor CPI-076…
6V8K 1.84 Å, Crystal structure of the p300 acetyltransferase domain with peptide-competitive…
4PZS 1.94 Å, Crystal structure of p300 histone acetyltransferase domain in complex with…
5KJ2 1.95 Å, The novel p300/CBP inhibitor A-485 uncovers a unique mechanism of action to target AR in…
6DS6 1.95 Å, Crystal structure of p300 ZZ domain in complex with histone H3 peptide
7QGS 2.0 Å, Crystal structure of p300 CH1 domain in complex with CITIF (a CITED2-HIF-1alpha hybrid)
7UGI 2.0 Å, Bromodomain of EP300 liganded with BMS-536924

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