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Zinc in PDB 7vhz: Crystal Structure of EP300 Hat Domain in Complex with Compound 7

Enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 7

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 7:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 7, PDB code: 7vhz 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) 19.98 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.676, 89.219, 91.132, 114.99, 95.33, 92.02
R / Rfree (%) 19.1 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7 (pdb code 7vhz). 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 7, PDB code: 7vhz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 1 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:52.9
occ:1.00
 ND1 A:HIS1255 2.1 53.2 1.0
SG A:CYS1258 2.3 47.6 1.0
SG A:CYS1163 2.3 59.7 1.0
SG A:CYS1164 2.3 57.8 1.0
CE1 A:HIS1255 3.1 58.1 1.0
CG A:HIS1255 3.1 52.0 1.0
CB A:CYS1164 3.3 57.7 1.0
CB A:HIS1255 3.4 43.1 1.0
CB A:CYS1258 3.5 41.3 1.0
N A:CYS1164 3.6 70.2 1.0
CA A:CYS1164 4.1 58.3 1.0
CB A:CYS1163 4.1 77.0 1.0
NE2 A:HIS1255 4.2 54.6 1.0
CD2 A:HIS1255 4.2 49.5 1.0
CD1 A:LEU1168 4.3 50.6 1.0
N A:HIS1255 4.4 50.0 1.0
O A:HOH2006 4.4 55.4 1.0
CA A:HIS1255 4.5 49.7 1.0
NH2 A:ARG1645 4.6 40.0 1.0
C A:CYS1163 4.6 71.9 1.0
CA A:CYS1163 4.8 80.4 1.0
CA A:CYS1258 4.9 42.3 1.0
N A:CYS1163 4.9 84.5 1.0
C A:CYS1164 5.0 61.5 1.0

Zinc binding site 2 out of 6 in 7vhz

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Zinc binding site 2 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:76.1
occ:1.00
 SG A:CYS1250 2.3 103.9 1.0
SG A:CYS1272 2.3 75.0 1.0
SG A:CYS1247 2.3 75.3 1.0
SG A:CYS1275 2.3 75.8 1.0
CB A:CYS1250 2.9 74.1 1.0
CB A:CYS1272 3.3 63.2 1.0
CB A:CYS1275 3.3 68.4 1.0
CB A:CYS1247 3.4 68.1 1.0
N A:CYS1250 3.5 81.8 1.0
CA A:CYS1250 3.8 78.0 1.0
N A:CYS1272 3.9 59.8 1.0
N A:CYS1275 3.9 79.1 1.0
CA A:CYS1272 4.1 65.0 1.0
CA A:CYS1275 4.2 75.2 1.0
C A:GLU1249 4.6 83.2 1.0
C A:CYS1272 4.6 70.4 1.0
O A:CYS1272 4.7 71.9 1.0
CB A:GLU1249 4.7 80.3 1.0
CA A:CYS1247 4.8 64.9 1.0
C A:CYS1250 5.0 75.1 1.0

Zinc binding site 3 out of 6 in 7vhz

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Zinc binding site 3 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:87.8
occ:1.00
 SG A:CYS1177 2.3 99.0 1.0
SG A:CYS1201 2.3 68.9 1.0
SG A:CYS1183 2.3 97.4 1.0
SG A:CYS1204 2.4 102.2 1.0
CB A:CYS1204 3.1 79.5 1.0
CB A:CYS1177 3.3 81.3 1.0
CB A:CYS1183 3.5 90.8 1.0
CB A:CYS1201 3.5 77.9 1.0
N A:CYS1204 4.2 86.9 1.0
CA A:CYS1204 4.3 84.1 1.0
N A:CYS1201 4.3 72.8 1.0
CA A:CYS1201 4.5 72.5 1.0
CB A:LYS1180 4.6 93.0 1.0
CE A:LYS1180 4.7 94.1 1.0
CA A:CYS1177 4.7 82.7 1.0
CA A:CYS1183 4.8 92.6 1.0
O A:CYS1201 4.9 77.6 1.0
NZ A:LYS1180 4.9 97.3 1.0
C A:CYS1201 5.0 76.3 1.0

Zinc binding site 4 out of 6 in 7vhz

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Zinc binding site 4 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:50.7
occ:1.00
 ND1 B:HIS1255 2.1 40.2 1.0
SG B:CYS1163 2.3 47.0 1.0
SG B:CYS1258 2.3 43.8 1.0
SG B:CYS1164 2.3 56.3 1.0
CG B:HIS1255 3.0 46.3 1.0
CE1 B:HIS1255 3.1 50.8 1.0
CB B:CYS1258 3.3 39.7 1.0
CB B:HIS1255 3.3 40.7 1.0
N B:CYS1164 3.4 74.9 1.0
CB B:CYS1164 3.5 62.7 1.0
CB B:CYS1163 3.6 56.2 1.0
CA B:CYS1164 4.1 62.4 1.0
CD2 B:HIS1255 4.2 43.7 1.0
NE2 B:HIS1255 4.2 50.5 1.0
N B:HIS1255 4.2 41.7 1.0
C B:CYS1163 4.2 71.8 1.0
CA B:HIS1255 4.4 44.0 1.0
NH2 B:ARG1166 4.4 60.2 1.0
CA B:CYS1163 4.5 75.4 1.0
CD1 B:LEU1168 4.5 42.0 1.0
NH2 B:ARG1645 4.6 39.0 1.0
CA B:CYS1258 4.7 42.5 1.0
C B:CYS1164 4.9 68.0 1.0
NE B:ARG1166 5.0 64.0 1.0
N B:CYS1163 5.0 76.0 1.0

Zinc binding site 5 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 5 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1702

b:77.3
occ:1.00
 SG B:CYS1250 2.3 80.3 1.0
SG B:CYS1272 2.3 72.6 1.0
SG B:CYS1247 2.3 76.9 1.0
SG B:CYS1275 2.3 75.7 1.0
CB B:CYS1247 3.3 64.1 1.0
CB B:CYS1250 3.3 65.6 1.0
CB B:CYS1275 3.4 68.2 1.0
CB B:CYS1272 3.5 68.0 1.0
N B:CYS1272 3.8 63.5 1.0
N B:CYS1250 3.9 75.5 1.0
CA B:CYS1272 4.2 57.5 1.0
N B:CYS1275 4.2 78.1 1.0
CA B:CYS1250 4.2 70.0 1.0
CA B:CYS1275 4.4 79.7 1.0
O B:CYS1272 4.6 68.0 1.0
CA B:CYS1247 4.7 62.8 1.0
C B:CYS1272 4.7 71.3 1.0
CB B:ARG1252 4.8 67.8 1.0
CG1 B:VAL1271 4.8 75.2 1.0
CB B:GLU1249 4.9 77.7 1.0
C B:VAL1271 4.9 64.6 1.0
C B:GLU1249 4.9 76.5 1.0

Zinc binding site 6 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 6 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1703

b:85.2
occ:1.00
 SG B:CYS1201 2.3 67.1 1.0
SG B:CYS1204 2.3 96.3 1.0
SG B:CYS1177 2.3 83.2 1.0
SG B:CYS1183 2.3 86.4 1.0
CB B:CYS1204 3.1 74.0 1.0
CB B:CYS1201 3.3 73.3 1.0
CB B:CYS1177 3.3 77.2 1.0
CB B:CYS1183 3.5 80.0 1.0
N B:CYS1201 4.1 72.4 1.0
N B:CYS1204 4.1 72.2 1.0
CA B:CYS1204 4.2 76.5 1.0
CA B:CYS1201 4.2 71.1 1.0
CB B:LYS1180 4.6 89.5 1.0
O B:CYS1201 4.7 72.9 1.0
CA B:CYS1177 4.8 80.6 1.0
C B:CYS1201 4.8 71.0 1.0
CA B:CYS1183 4.8 88.3 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: Wed Oct 30 12:39:35 2024

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