Zinc in PDB 7nd1: First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain

Enzymatic activity of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain

All present enzymatic activity of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain:
2.3.2.27;

Other elements in 7nd1:

The structure of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain also contains other interesting chemical elements:

Chlorine (Cl) 20 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain (pdb code 7nd1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain, PDB code: 7nd1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7nd1

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Zinc binding site 1 out of 4 in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:0.3
occ:1.00
SG A:CYS90 2.1 0.4 1.0
ND1 A:HIS69 2.1 0.3 1.0
SG A:CYS67 2.3 0.3 1.0
SG A:CYS87 2.6 0.4 1.0
HE1 A:HIS69 2.6 0.4 1.0
CE1 A:HIS69 2.7 0.4 1.0
HB3 A:CYS87 2.7 0.3 1.0
HB2 A:CYS67 2.9 0.4 1.0
CB A:CYS87 3.0 0.3 1.0
H A:CYS90 3.1 0.4 1.0
CB A:CYS67 3.1 0.4 1.0
HB2 A:CYS87 3.1 0.3 1.0
CG A:HIS69 3.3 0.3 1.0
HG1 A:THR64 3.4 0.3 1.0
HB3 A:CYS67 3.5 0.4 1.0
HB2 A:HIS69 3.5 0.3 1.0
HB A:THR89 3.5 0.4 1.0
CB A:CYS90 3.6 0.5 1.0
HB3 A:CYS90 3.7 0.5 1.0
NE2 A:HIS69 3.9 0.4 1.0
N A:CYS90 3.9 0.4 1.0
CB A:HIS69 3.9 0.3 1.0
OG1 A:THR64 4.1 0.3 1.0
CD2 A:HIS69 4.2 0.4 1.0
HB2 A:CYS90 4.3 0.5 1.0
H A:THR89 4.3 0.4 1.0
CA A:CYS90 4.3 0.4 1.0
HB3 A:HIS69 4.3 0.3 1.0
HG21 A:THR64 4.4 0.3 1.0
CA A:CYS87 4.5 0.3 1.0
CB A:THR89 4.5 0.4 1.0
CA A:CYS67 4.5 0.4 1.0
HE2 A:HIS69 4.6 0.4 1.0
HB3 A:LYS92 4.6 0.4 1.0
HZ A:PHE71 4.7 0.3 1.0
HG1 A:THR89 4.7 0.4 1.0
H A:ARG91 4.8 0.4 1.0
C A:CYS67 4.9 0.4 1.0
O A:CYS67 4.9 0.4 1.0
HB2 A:LYS92 4.9 0.4 1.0
HA A:CYS87 4.9 0.3 1.0
C A:THR89 4.9 0.4 1.0
H A:LYS92 4.9 0.4 1.0
C A:CYS87 4.9 0.3 1.0
O A:CYS87 4.9 0.3 1.0
C A:CYS90 5.0 0.4 1.0
N A:THR89 5.0 0.4 1.0

Zinc binding site 2 out of 4 in 7nd1

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Zinc binding site 2 out of 4 in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:0.5
occ:1.00
SG A:CYS75 2.2 0.5 1.0
SG A:CYS72 2.3 0.5 1.0
SG A:CYS51 2.3 0.4 1.0
SG A:CYS54 2.4 0.5 1.0
HB2 A:CYS72 2.6 0.4 1.0
HB3 A:CYS51 2.8 0.4 1.0
CB A:CYS51 3.0 0.4 1.0
CB A:CYS72 3.0 0.4 1.0
HB2 A:CYS75 3.0 0.4 1.0
HB2 A:CYS51 3.1 0.4 1.0
CB A:CYS75 3.1 0.4 1.0
HB3 A:CYS54 3.4 0.5 1.0
H A:CYS54 3.4 0.5 1.0
HB3 A:CYS75 3.4 0.4 1.0
HB A:ILE53 3.4 0.4 1.0
H A:CYS72 3.5 0.4 1.0
CB A:CYS54 3.5 0.5 1.0
HB3 A:CYS72 3.6 0.4 1.0
N A:CYS54 4.0 0.5 1.0
N A:CYS72 4.1 0.4 1.0
CA A:CYS72 4.1 0.4 1.0
HD12 A:ILE53 4.2 0.4 1.0
HB2 A:CYS54 4.3 0.5 1.0
CA A:CYS54 4.4 0.5 1.0
CB A:ILE53 4.4 0.4 1.0
CA A:CYS51 4.4 0.4 1.0
H A:CYS75 4.5 0.4 1.0
H A:ILE53 4.5 0.4 1.0
HG22 A:ILE53 4.5 0.4 1.0
CA A:CYS75 4.6 0.4 1.0
HD23 A:LEU58 4.6 0.4 1.0
HG21 A:ILE53 4.7 0.4 1.0
HA A:CYS72 4.7 0.4 1.0
HA A:LEU58 4.8 0.5 1.0
CG2 A:ILE53 4.8 0.4 1.0
H A:CYS51 4.9 0.5 1.0
O A:CYS51 4.9 0.5 1.0
HA A:CYS51 4.9 0.4 1.0
N A:CYS75 4.9 0.4 1.0
C A:CYS51 4.9 0.4 1.0
CD1 A:ILE53 5.0 0.4 1.0
HA A:CYS75 5.0 0.4 1.0
H A:LYS59 5.0 0.5 1.0
H A:LEU55 5.0 0.5 1.0

Zinc binding site 3 out of 4 in 7nd1

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Zinc binding site 3 out of 4 in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1201

b:0.9
occ:1.00
HB3 H:CYS1021 1.8 0.9 1.0
HB2 H:CYS1021 1.8 0.9 1.0
CB H:CYS1021 2.1 0.9 1.0
SG H:CYS1042 2.3 0.9 1.0
SG H:CYS1018 2.3 0.8 1.0
SG H:CYS1039 2.4 0.8 1.0
HB3 H:CYS1018 2.5 0.8 1.0
CB H:CYS1018 2.8 0.8 1.0
HB2 H:CYS1039 2.9 0.8 1.0
H H:CYS1021 2.9 0.9 1.0
HB2 H:CYS1018 3.0 0.8 1.0
CB H:CYS1039 3.2 0.8 1.0
SG H:CYS1021 3.2 0.9 1.0
H H:CYS1039 3.3 0.8 1.0
CA H:CYS1021 3.4 0.9 1.0
N H:CYS1021 3.5 0.9 1.0
HH12 A:ARG26 3.6 0.9 1.0
CB H:CYS1042 3.7 0.8 1.0
HB2 H:CYS1042 3.8 0.8 1.0
HB3 H:CYS1039 3.8 0.8 1.0
HA H:CYS1021 4.0 0.9 1.0
HB3 H:CYS1042 4.0 0.8 1.0
N H:CYS1039 4.1 0.8 1.0
HB2 H:LEU1020 4.1 0.9 1.0
CA H:CYS1018 4.3 0.8 1.0
CA H:CYS1039 4.3 0.8 1.0
NH1 A:ARG26 4.4 0.9 1.0
HH22 A:ARG26 4.5 0.9 1.0
C H:CYS1021 4.5 1.0 1.0
H H:GLY1023 4.6 1.0 1.0
H H:LEU1020 4.6 0.9 1.0
H H:CYS1018 4.6 0.8 1.0
C H:LEU1020 4.7 0.9 1.0
O H:CYS1018 4.7 0.9 1.0
C H:CYS1018 4.7 0.8 1.0
HA H:PHE1025 4.7 0.8 1.0
O H:TYR1024 4.7 0.9 1.0
H H:CYS1042 4.8 0.8 1.0
O H:GLY1023 4.8 0.9 1.0
HA H:CYS1018 4.8 0.8 1.0
HA H:CYS1039 4.8 0.8 1.0
HH11 A:ARG26 4.8 0.9 1.0
HD1 H:PHE1025 4.9 0.7 1.0
H H:GLY1022 4.9 1.0 1.0
H H:ILE1026 4.9 0.8 1.0
HB3 H:PHE1038 5.0 0.7 1.0
N H:CYS1018 5.0 0.8 1.0
CB H:LEU1020 5.0 0.9 1.0

Zinc binding site 4 out of 4 in 7nd1

Go back to Zinc Binding Sites List in 7nd1
Zinc binding site 4 out of 4 in the First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of First-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1202

b:0.6
occ:1.00
ND1 H:HIS1036 2.2 0.6 1.0
SG H:CYS1034 2.3 0.6 1.0
SG H:CYS1056 2.3 0.7 1.0
SG H:CYS1053 2.3 0.7 1.0
HB2 H:HIS1036 2.8 0.6 1.0
HB2 H:CYS1034 2.9 0.6 1.0
H H:CYS1056 3.0 0.8 1.0
HB2 H:CYS1053 3.0 0.7 1.0
CG H:HIS1036 3.0 0.6 1.0
CB H:CYS1034 3.1 0.6 1.0
CE1 H:HIS1036 3.1 0.7 1.0
CB H:CYS1053 3.1 0.7 1.0
HB3 H:CYS1053 3.2 0.7 1.0
HB3 H:CYS1056 3.2 0.7 1.0
HE1 H:HIS1036 3.3 0.7 1.0
CB H:CYS1056 3.4 0.7 1.0
HB3 H:CYS1034 3.4 0.6 1.0
CB H:HIS1036 3.4 0.6 1.0
HG22 H:VAL1058 3.5 0.6 1.0
N H:CYS1056 3.7 0.8 1.0
HB3 H:HIS1036 3.9 0.6 1.0
CD2 H:HIS1036 4.0 0.7 1.0
NE2 H:HIS1036 4.0 0.7 1.0
CA H:CYS1056 4.1 0.8 1.0
HD12 H:ILE1031 4.2 0.6 1.0
HB2 H:CYS1056 4.2 0.7 1.0
H H:ASP1057 4.2 0.8 1.0
HB H:ILE1055 4.2 0.8 1.0
HG21 H:VAL1058 4.2 0.6 1.0
H H:HIS1036 4.2 0.6 1.0
CG2 H:VAL1058 4.3 0.6 1.0
H H:ILE1055 4.4 0.8 1.0
H H:VAL1058 4.4 0.7 1.0
CA H:CYS1034 4.5 0.5 1.0
CA H:CYS1053 4.6 0.7 1.0
CA H:HIS1036 4.6 0.6 1.0
N H:HIS1036 4.6 0.6 1.0
HG23 H:VAL1058 4.7 0.6 1.0
HZ H:PHE1038 4.7 0.7 1.0
N H:ASP1057 4.7 0.8 1.0
HB H:ILE1031 4.7 0.6 1.0
C H:CYS1034 4.8 0.5 1.0
HD2 H:HIS1036 4.8 0.7 1.0
H H:CYS1034 4.8 0.5 1.0
C H:CYS1056 4.8 0.8 1.0
HA H:CYS1053 4.9 0.7 1.0
HA H:CYS1056 4.9 0.8 1.0
HD13 H:ILE1031 4.9 0.6 1.0
O H:CYS1034 4.9 0.6 1.0
HG13 H:VAL1058 4.9 0.7 1.0
C H:ILE1055 4.9 0.8 1.0
HG21 H:ILE1031 4.9 0.6 1.0
CD1 H:ILE1031 5.0 0.6 1.0
HD2 H:PRO1054 5.0 0.7 1.0

Reference:

T.Cierpicki, G.Lung, L.Jaremko. Titlefirst-in-Class Small Molecule Inhibitors of Polycomb Repressive Complex 1 (PRC1) Ring Domain To Be Published.
Page generated: Mon Jul 12 17:26:10 2021

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