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Zinc in PDB 8gzc: Crystal Structure of EP300 Hat Domain in Complex with Compound 10

Enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 10

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 10:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 10, PDB code: 8gzc 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) 19.91 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.5, 89.35, 91.6, 116.6, 95.18, 91.78
R / Rfree (%) 19.5 / 22.7

Other elements in 8gzc:

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 10 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10 (pdb code 8gzc). 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 10, PDB code: 8gzc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8gzc

Go back to Zinc Binding Sites List in 8gzc
Zinc binding site 1 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:76.2
occ:1.00
 ND1 A:HIS1255 2.1 73.0 1.0
SG A:CYS1163 2.3 78.2 1.0
SG A:CYS1164 2.3 75.6 1.0
SG A:CYS1258 2.3 64.5 1.0
CG A:HIS1255 3.0 72.2 1.0
CE1 A:HIS1255 3.2 78.7 1.0
CB A:HIS1255 3.2 62.8 1.0
CB A:CYS1258 3.4 60.0 1.0
N A:CYS1164 3.5 91.0 1.0
CB A:CYS1163 3.5 110.7 1.0
CB A:CYS1164 3.7 97.4 1.0
CD2 A:HIS1255 4.2 75.2 1.0
NE2 A:HIS1255 4.2 78.0 1.0
CA A:CYS1164 4.3 87.3 1.0
N A:CYS1163 4.3 105.8 1.0
CA A:CYS1163 4.3 105.7 1.0
NH2 A:ARG1645 4.4 64.1 1.0
CD1 A:LEU1168 4.4 61.2 1.0
C A:CYS1163 4.5 101.3 1.0
CA A:HIS1255 4.5 72.8 1.0
N A:HIS1255 4.5 64.6 1.0
CA A:CYS1258 4.8 64.2 1.0

Zinc binding site 2 out of 6 in 8gzc

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Zinc binding site 2 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:115.7
occ:1.00
 SG A:CYS1250 2.3 101.0 1.0
SG A:CYS1275 2.3 112.1 1.0
SG A:CYS1247 2.3 105.7 1.0
SG A:CYS1272 2.3 103.8 1.0
CB A:CYS1272 3.2 104.0 1.0
CB A:CYS1247 3.3 94.4 1.0
CB A:CYS1250 3.3 104.0 1.0
CB A:CYS1275 3.3 104.2 1.0
N A:CYS1250 3.7 104.9 1.0
N A:CYS1272 3.8 94.5 1.0
CA A:CYS1272 4.0 97.7 1.0
N A:CYS1275 4.0 112.6 1.0
CA A:CYS1250 4.1 106.0 1.0
CA A:CYS1275 4.3 113.9 1.0
C A:CYS1272 4.5 103.8 1.0
O A:CYS1272 4.5 107.5 1.0
CA A:CYS1247 4.7 92.9 1.0
CB A:GLU1249 4.7 108.9 1.0
C A:GLU1249 4.8 104.8 1.0
C A:CYS1250 4.9 104.0 1.0
C A:VAL1271 4.9 92.9 1.0

Zinc binding site 3 out of 6 in 8gzc

Go back to Zinc Binding Sites List in 8gzc
Zinc binding site 3 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:111.3
occ:1.00
 SG A:CYS1177 2.3 118.1 1.0
SG A:CYS1204 2.3 116.6 1.0
SG A:CYS1183 2.3 106.2 1.0
SG A:CYS1201 2.3 97.7 1.0
CB A:CYS1177 2.9 112.9 1.0
CB A:CYS1204 3.3 116.3 1.0
CB A:CYS1201 3.3 105.6 1.0
CB A:CYS1183 3.4 102.9 1.0
N A:CYS1201 4.2 100.6 1.0
N A:CYS1204 4.3 105.4 1.0
CA A:CYS1201 4.3 105.1 1.0
CA A:CYS1204 4.4 112.5 1.0
CA A:CYS1177 4.4 116.5 1.0
CB A:LYS1180 4.6 105.4 1.0
CA A:CYS1183 4.7 104.3 1.0
O A:CYS1201 4.9 102.1 1.0
C A:CYS1201 4.9 101.8 1.0
C A:CYS1177 5.0 118.4 1.0
C A:CYS1183 5.0 101.8 1.0
O A:THR1184 5.0 102.3 1.0

Zinc binding site 4 out of 6 in 8gzc

Go back to Zinc Binding Sites List in 8gzc
Zinc binding site 4 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:81.2
occ:1.00
 ND1 B:HIS1255 2.1 70.6 1.0
SG B:CYS1163 2.3 66.1 1.0
SG B:CYS1164 2.3 82.0 1.0
SG B:CYS1258 2.3 66.3 1.0
CG B:HIS1255 3.0 66.2 1.0
CE1 B:HIS1255 3.0 77.6 1.0
CB B:CYS1163 3.2 85.4 1.0
CB B:HIS1255 3.3 56.5 1.0
CB B:CYS1164 3.4 87.3 1.0
CB B:CYS1258 3.5 62.4 1.0
N B:CYS1164 3.7 104.0 1.0
CD1 B:LEU1168 3.8 67.7 1.0
NE2 B:HIS1255 4.1 80.0 1.0
CD2 B:HIS1255 4.1 72.8 1.0
NH2 B:ARG1166 4.1 70.8 1.0
CA B:CYS1164 4.2 91.5 1.0
NH2 B:ARG1645 4.2 59.0 1.0
C B:CYS1163 4.3 106.5 1.0
CA B:CYS1163 4.4 106.8 1.0
CA B:HIS1255 4.6 66.0 1.0
NE B:ARG1166 4.7 69.0 1.0
N B:HIS1255 4.7 67.0 1.0
CA B:CYS1258 4.9 65.5 1.0
CZ B:ARG1166 4.9 79.9 1.0
CZ B:ARG1645 4.9 62.3 1.0

Zinc binding site 5 out of 6 in 8gzc

Go back to Zinc Binding Sites List in 8gzc
Zinc binding site 5 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:119.0
occ:1.00
 SG B:CYS1247 2.3 109.2 1.0
SG B:CYS1250 2.3 95.4 1.0
SG B:CYS1275 2.3 127.2 1.0
SG B:CYS1272 2.3 109.7 1.0
CB B:CYS1247 3.3 105.4 1.0
CB B:CYS1250 3.3 113.1 1.0
CB B:CYS1275 3.4 105.2 1.0
CB B:CYS1272 3.5 110.9 1.0
N B:CYS1250 3.8 113.8 1.0
N B:CYS1275 4.0 124.2 1.0
N B:CYS1272 4.0 97.4 1.0
CA B:CYS1250 4.1 112.5 1.0
CA B:CYS1272 4.2 98.7 1.0
CA B:CYS1275 4.3 121.9 1.0
CB B:GLU1249 4.6 104.5 1.0
O B:CYS1272 4.7 118.1 1.0
CB B:ARG1252 4.7 86.2 1.0
C B:CYS1272 4.7 108.8 1.0
C B:GLU1249 4.8 118.8 1.0
CA B:CYS1247 4.8 103.1 1.0
C B:CYS1250 4.8 108.5 1.0
N B:GLY1251 4.9 105.6 1.0
N B:ARG1252 5.0 86.7 1.0
C B:GLY1274 5.0 122.5 1.0

Zinc binding site 6 out of 6 in 8gzc

Go back to Zinc Binding Sites List in 8gzc
Zinc binding site 6 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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

b:148.2
occ:1.00
 SG B:CYS1177 2.3 140.0 1.0
SG B:CYS1204 2.3 148.7 1.0
SG B:CYS1201 2.3 117.8 1.0
SG B:CYS1183 2.3 139.7 1.0
CB B:CYS1177 3.1 127.7 1.0
CB B:CYS1204 3.3 128.3 1.0
CB B:CYS1201 3.3 124.8 1.0
CB B:CYS1183 3.5 126.1 1.0
N B:CYS1204 4.1 118.8 1.0
CA B:CYS1204 4.3 123.4 1.0
N B:CYS1201 4.3 126.5 1.0
CA B:CYS1201 4.3 129.3 1.0
CA B:CYS1177 4.6 127.9 1.0
O B:CYS1201 4.8 130.9 1.0
CA B:CYS1183 4.8 126.2 1.0
C B:CYS1201 4.8 127.0 1.0

Reference:

R.Kanada, Y.Kagoshima, T.Suzuki, A.Nakamura, H.Funami, J.Watanabe, M.Asano, M.Takahashi, O.Ubukata, K.Suzuki, T.Aikawa, K.Sato, M.Goto, G.Setsu, K.Ito, K.Kihara, M.Kuroha, T.Kohno, H.Ogiwara, T.Isoyama, Y.Tominaga, S.Higuchi, H.Naito. Discovery of Ds-9300: A Highly Potent, Selective, and Once-Daily Oral EP300/Cbp Histone Acetyltransferase Inhibitor. J.Med.Chem. 2022.
ISSN: ISSN 0022-2623
PubMed: 36572866
DOI: 10.1021/ACS.JMEDCHEM.2C01641
Page generated: Thu Oct 31 06:50:36 2024

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