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Zinc in PDB 7vhy: Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3

Enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3, PDB code: 7vhy was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.49, 88.781, 89.949, 116.58, 99.44, 85.3
R / Rfree (%) 21.2 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 (pdb code 7vhy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3, PDB code: 7vhy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7vhy

Go back to Zinc Binding Sites List in 7vhy
Zinc binding site 1 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:66.8
occ:1.00
 ND1 A:HIS1255 2.1 57.8 1.0
SG A:CYS1258 2.3 55.6 1.0
SG A:CYS1163 2.3 74.8 1.0
SG A:CYS1164 2.3 70.0 1.0
CG A:HIS1255 3.0 57.4 1.0
CE1 A:HIS1255 3.1 61.0 1.0
CB A:HIS1255 3.2 55.6 1.0
CB A:CYS1258 3.3 49.5 1.0
CB A:CYS1163 3.6 87.9 1.0
N A:CYS1164 3.7 91.0 1.0
CB A:CYS1164 3.8 86.8 1.0
CD2 A:HIS1255 4.2 58.9 1.0
NE2 A:HIS1255 4.2 59.0 1.0
CA A:CYS1164 4.4 84.5 1.0
N A:HIS1255 4.4 59.5 1.0
NH2 A:ARG1645 4.4 49.7 1.0
C A:CYS1163 4.4 98.9 1.0
CA A:HIS1255 4.4 54.5 1.0
CA A:CYS1163 4.4 97.6 1.0
CD1 A:LEU1168 4.7 55.3 1.0
CA A:CYS1258 4.7 51.8 1.0
N A:CYS1163 4.7 90.6 1.0

Zinc binding site 2 out of 6 in 7vhy

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Zinc binding site 2 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:93.7
occ:1.00
 SG A:CYS1275 2.3 91.2 1.0
SG A:CYS1272 2.3 85.7 1.0
SG A:CYS1250 2.3 96.2 1.0
SG A:CYS1247 2.3 75.4 1.0
CB A:CYS1250 2.6 83.1 1.0
N A:CYS1250 3.3 88.4 1.0
CB A:CYS1275 3.4 86.4 1.0
CB A:CYS1272 3.5 76.1 1.0
CA A:CYS1250 3.5 83.8 1.0
CB A:CYS1247 3.6 79.6 1.0
N A:CYS1275 4.1 85.6 1.0
N A:CYS1272 4.1 71.2 1.0
CA A:CYS1272 4.3 74.9 1.0
CA A:CYS1275 4.3 86.0 1.0
C A:GLU1249 4.5 86.0 1.0
CB A:GLU1249 4.7 87.3 1.0
C A:CYS1250 4.8 84.0 1.0
C A:CYS1272 4.8 80.0 1.0
O A:CYS1272 4.9 77.9 1.0
CA A:CYS1247 5.0 77.2 1.0

Zinc binding site 3 out of 6 in 7vhy

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Zinc binding site 3 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:127.2
occ:1.00
 SG A:CYS1177 2.3 112.7 1.0
SG A:CYS1204 2.3 116.7 1.0
SG A:CYS1183 2.3 131.7 1.0
SG A:CYS1201 2.3 142.3 1.0
CB A:CYS1201 2.6 110.8 1.0
CB A:CYS1177 2.8 114.3 1.0
CB A:CYS1183 3.0 119.8 1.0
CB A:CYS1204 3.7 103.8 1.0
CA A:CYS1201 4.0 107.2 1.0
N A:CYS1201 4.2 107.1 1.0
CA A:CYS1177 4.3 111.7 1.0
CA A:CYS1183 4.4 116.3 1.0
C A:CYS1183 4.7 114.6 1.0
N A:CYS1204 4.8 105.4 1.0
CA A:CYS1204 4.9 103.0 1.0
C A:CYS1177 4.9 109.1 1.0

Zinc binding site 4 out of 6 in 7vhy

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Zinc binding site 4 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:54.6
occ:1.00
 ND1 B:HIS1255 2.1 56.7 1.0
SG B:CYS1163 2.3 58.5 1.0
SG B:CYS1258 2.3 51.0 1.0
SG B:CYS1164 2.3 71.5 1.0
CG B:HIS1255 3.1 52.3 1.0
CE1 B:HIS1255 3.1 56.4 1.0
CB B:HIS1255 3.4 47.5 1.0
CB B:CYS1258 3.5 46.6 1.0
CB B:CYS1164 3.7 79.6 1.0
N B:CYS1164 3.8 78.3 1.0
CB B:CYS1163 3.8 75.2 1.0
NE2 B:HIS1255 4.2 54.4 1.0
CD2 B:HIS1255 4.2 55.1 1.0
CA B:CYS1164 4.4 78.5 1.0
NH2 B:ARG1645 4.4 48.7 1.0
CD1 B:LEU1168 4.5 55.1 1.0
C B:CYS1163 4.5 78.0 1.0
N B:HIS1255 4.5 49.6 1.0
CA B:HIS1255 4.6 49.9 1.0
CA B:CYS1163 4.6 79.7 1.0
N B:CYS1163 4.8 80.6 1.0
CA B:CYS1258 4.8 43.9 1.0
NH2 B:ARG1166 4.9 65.8 1.0

Zinc binding site 5 out of 6 in 7vhy

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Zinc binding site 5 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1702

b:91.7
occ:1.00
 SG B:CYS1275 2.3 92.0 1.0
SG B:CYS1272 2.3 78.7 1.0
SG B:CYS1250 2.3 98.8 1.0
SG B:CYS1247 2.3 80.4 1.0
CB B:CYS1250 2.7 75.0 1.0
N B:CYS1250 3.3 91.7 1.0
CB B:CYS1275 3.4 82.5 1.0
CA B:CYS1250 3.6 85.6 1.0
CB B:CYS1272 3.6 76.3 1.0
CB B:CYS1247 3.6 81.7 1.0
N B:CYS1275 4.0 82.4 1.0
N B:CYS1272 4.1 71.9 1.0
CA B:CYS1275 4.2 83.0 1.0
CA B:CYS1272 4.4 71.2 1.0
C B:GLU1249 4.5 97.8 1.0
CB B:GLU1249 4.6 93.2 1.0
O B:CYS1272 4.8 74.5 1.0
C B:CYS1272 4.8 73.8 1.0
C B:CYS1250 4.9 82.8 1.0
CA B:GLU1249 5.0 96.2 1.0
CA B:CYS1247 5.0 79.1 1.0

Zinc binding site 6 out of 6 in 7vhy

Go back to Zinc Binding Sites List in 7vhy
Zinc binding site 6 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of EP300 Hat Domain in Complex with Compound (+)-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1703

b:91.4
occ:1.00
 SG B:CYS1177 2.3 88.9 1.0
SG B:CYS1204 2.3 124.7 1.0
SG B:CYS1201 2.3 93.2 1.0
SG B:CYS1183 2.3 80.6 1.0
CB B:CYS1204 2.9 93.4 1.0
CB B:CYS1201 3.1 84.1 1.0
CB B:CYS1177 3.3 85.9 1.0
CB B:CYS1183 3.6 91.9 1.0
N B:CYS1204 4.0 94.9 1.0
CA B:CYS1204 4.0 96.0 1.0
CA B:CYS1201 4.2 82.8 1.0
N B:CYS1201 4.2 82.2 1.0
O B:CYS1201 4.7 87.8 1.0
CA B:CYS1177 4.7 89.8 1.0
C B:CYS1201 4.8 83.6 1.0

Reference:

R.Kanada, Y.Kagoshima, M.Asano, T.Suzuki, T.Murata, M.Haruta, M.Takahashi, O.Ubukata, K.Hashimoto, K.Obata, K.Kihara, M.Kuroha, T.Banjo, N.Togashi, K.Sato, Y.Yamamoto, K.Suzuki, T.Isoyama, Y.Tominaga, S.Higuchi, H.Naito. Discovery of EP300/Cbp Histone Acetyltransferase Inhibitors Through Scaffold Hopping of 1,4-Oxazepane Ring. Bioorg.Med.Chem.Lett. V. 66 28726 2022.
ISSN: ESSN 1464-3405
PubMed: 35413416
DOI: 10.1016/J.BMCL.2022.128726
Page generated: Fri Aug 22 05:40:16 2025

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