Receptor
PDB id Resolution Class Description Source Keywords
6JY3 1.85 Å EC: 1.9.3.1 MONOMERIC FORM OF BOVINE HEART CYTOCHROME C OXIDASE IN THE F OXIDIZED STATE BOS TAURUS MONOMER FULLY OXIDIZED OXIDOREDUCTASE
Ref.: MONOMERIC STRUCTURE OF AN ACTIVE FORM OF BOVINE CYTOCHROMECOXIDASE. PROC.NATL.ACAD.SCI.USA V. 116 19945 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CQX A:611;
A:609;
C:306;
B:304;
B:303;
C:307;
G:101;
A:610;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
none;
none;
none;
submit data
364.474 C18 H36 O7 CCCCC...
PEK C:303;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
768.055 C43 H78 N O8 P CCCCC...
CDL C:305;
A:606;
B:301;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
1464.04 C81 H156 O17 P2 CCCCC...
MG A:604;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PGV A:608;
C:304;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0;
submit data
749.007 C40 H77 O10 P CCCCC...
PER A:607;
Invalid;
none;
submit data
31.999 O2 [O-][...
ZN F:101;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
NA C:302;
A:605;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
HEA A:602;
A:601;
Part of Protein;
Part of Protein;
none;
none;
submit data
852.837 C49 H56 Fe N4 O6 Cc1c2...
CHD C:301;
Valid;
none;
submit data
408.571 C24 H40 O5 C[C@H...
CU A:603;
Part of Protein;
none;
submit data
63.546 Cu [Cu+2...
CUA B:302;
Part of Protein;
none;
submit data
127.092 Cu2 [Cu][...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6JY3 1.85 Å EC: 1.9.3.1 MONOMERIC FORM OF BOVINE HEART CYTOCHROME C OXIDASE IN THE F OXIDIZED STATE BOS TAURUS MONOMER FULLY OXIDIZED OXIDOREDUCTASE
Ref.: MONOMERIC STRUCTURE OF AN ACTIVE FORM OF BOVINE CYTOCHROMECOXIDASE. PROC.NATL.ACAD.SCI.USA V. 116 19945 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6JY3 - PEK C43 H78 N O8 P CCCCCCCCCC....
2 6JY4 - PGV C40 H77 O10 P CCCCCCCCCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6JY3 - PEK C43 H78 N O8 P CCCCCCCCCC....
2 6JY4 - PGV C40 H77 O10 P CCCCCCCCCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 6JY3 - PEK C43 H78 N O8 P CCCCCCCCCC....
2 6JY4 - PGV C40 H77 O10 P CCCCCCCCCC....
3 2Y69 - CHD C24 H40 O5 C[C@H](CCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CQX; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 CQX 1 1
2 BNG 0.740741 0.97561
3 HSJ 0.740741 0.97561
4 BOG 0.740741 0.97561
5 B7G 0.722222 0.97561
6 KGM 0.722222 0.97561
7 JZR 0.672727 0.951219
8 GLC HEX 0.672727 0.951219
9 BHG 0.672727 0.951219
10 AFO 0.654545 0.883721
11 DEG 0.589286 0.878049
12 LMT 0.558824 0.930233
13 DMU 0.558824 0.930233
14 LMU 0.558824 0.930233
15 UMQ 0.558824 0.930233
16 L6T 0.544118 0.953488
17 DR4 0.514706 0.883721
18 XNS 0.514706 0.883721
19 FK9 0.484848 0.928571
20 EBQ 0.467742 0.809524
21 BGB 0.45 0.909091
22 BHE 0.447368 0.909091
23 EBG 0.444444 0.767442
24 GLA GAL GLC NBU 0.444444 0.860465
25 GLA GAL BGC 5VQ 0.422535 0.813953
26 FEE 0.418605 0.740741
27 SOG 0.41791 0.863636
28 BGL 0.41791 0.97561
29 OPM MAN MAN 0.417722 0.906977
30 CE1 0.413793 0.619048
31 N8E 0.413793 0.619048
32 CE9 0.413793 0.619048
33 C8E 0.413793 0.619048
34 32M 0.413793 0.619048
35 C10 0.413793 0.619048
36 GM3 0.411765 0.754717
37 T6D 0.410256 0.909091
38 10M 0.410256 0.869565
39 HTG 0.402985 0.863636
40 FUC BHG 0.402597 0.909091
41 BHG FUC 0.402597 0.909091
42 4YA 0.402597 0.909091
43 0SH 0.402299 0.740741
44 AGH 0.402299 0.740741
45 F61 0.402299 0.740741
46 PBS 0.402299 0.740741
47 1O2 0.4 0.888889
48 AOG FUC 0.4 0.754717
Ligand no: 2; Ligand: PEK; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 PEK 1 1
2 GP7 0.873418 1
3 ZPE 0.844156 1
4 L9Q 0.818182 1
5 6OU 0.818182 1
6 LOP 0.818182 1
7 PSC 0.785714 0.79661
8 PEH 0.77027 0.980769
9 PEV 0.77027 0.980769
10 8PE 0.77027 0.980769
11 PEF 0.77027 0.980769
12 PTY 0.77027 0.980769
13 9PE 0.76 0.980769
14 EPH 0.741573 1
15 T7X 0.727273 0.711864
16 PCW 0.682353 0.79661
17 PGW 0.639535 0.830189
18 D3D 0.639535 0.830189
19 P50 0.636364 0.924528
20 PX4 0.634146 0.779661
21 LIO 0.634146 0.779661
22 HGX 0.634146 0.779661
23 6PL 0.634146 0.779661
24 HGP 0.634146 0.779661
25 PLD 0.634146 0.779661
26 PC7 0.634146 0.779661
27 DR9 0.632184 0.830189
28 PGV 0.632184 0.830189
29 PEE 0.62963 0.962264
30 P6L 0.625 0.830189
31 OZ2 0.617977 0.830189
32 D21 0.609756 0.792453
33 CD4 0.604938 0.807692
34 DLP 0.602151 0.728814
35 P5S 0.595238 0.888889
36 PGT 0.590361 0.811321
37 LHG 0.590361 0.811321
38 XP5 0.590361 0.779661
39 BQ9 0.583333 0.615385
40 B7N 0.576087 0.711864
41 PCK 0.55914 0.741935
42 6PH 0.556962 0.773585
43 3PH 0.556962 0.773585
44 LPP 0.556962 0.773585
45 F57 0.556962 0.773585
46 7PH 0.556962 0.773585
47 CN3 0.550562 0.807692
48 PX8 0.55 0.754717
49 PX2 0.55 0.754717
50 7P9 0.55 0.773585
51 HXG 0.547619 0.779661
52 CN6 0.545455 0.807692
53 PA8 0.5375 0.754717
54 PIE 0.536842 0.666667
55 POV 0.531915 0.728814
56 L9R 0.531915 0.728814
57 PII 0.52809 0.694915
58 PGK 0.521277 0.767857
59 P3A 0.520833 0.796296
60 PD7 0.5125 0.773585
61 PSF 0.511628 0.888889
62 3PE 0.511364 0.867925
63 44G 0.505882 0.811321
64 CDL 0.505747 0.735849
65 DGG 0.505155 0.767857
66 PIO 0.5 0.683333
67 PIF 0.5 0.683333
68 52N 0.5 0.683333
69 8ND 0.5 0.716981
70 M7U 0.5 0.773585
71 PIZ 0.494737 0.694915
72 42H 0.494624 0.830508
73 IP9 0.484211 0.694915
74 MC3 0.483516 0.711864
75 PC1 0.483516 0.711864
76 PCF 0.483516 0.711864
77 PDK 0.481132 0.819672
78 44E 0.469136 0.773585
79 S12 0.468085 0.888889
80 1AG 0.463415 0.603774
81 NKP 0.45977 0.792453
82 AGA 0.456522 0.777778
83 LPC 0.444444 0.813559
84 LAP 0.444444 0.813559
85 LP3 0.444444 0.813559
86 OPC 0.417476 0.783333
87 OLC 0.411765 0.603774
88 OLB 0.411765 0.603774
89 NKN 0.404762 0.773585
90 NKO 0.404762 0.773585
Ligand no: 3; Ligand: PGV; Similar ligands found: 110
No: Ligand ECFP6 Tc MDL keys Tc
1 PGV 1 1
2 DR9 1 1
3 D3D 0.985507 1
4 PGW 0.985507 1
5 OZ2 0.971831 1
6 P6L 0.957747 1
7 LHG 0.855072 0.977778
8 PGT 0.855072 0.977778
9 LOP 0.766234 0.830189
10 6OU 0.766234 0.830189
11 L9Q 0.766234 0.830189
12 P50 0.75 0.826923
13 CD4 0.75 0.933333
14 ZPE 0.746835 0.830189
15 44G 0.746479 0.977778
16 PCW 0.7375 0.706897
17 PGK 0.7375 0.916667
18 P3A 0.731707 0.956522
19 D21 0.72973 0.913043
20 DGG 0.710843 0.916667
21 B7N 0.678571 0.843137
22 CN3 0.675 0.933333
23 GP7 0.674419 0.830189
24 PSC 0.659091 0.706897
25 CN6 0.65 0.933333
26 PEH 0.649351 0.811321
27 PTY 0.649351 0.811321
28 PEV 0.649351 0.811321
29 8PE 0.649351 0.811321
30 PEF 0.649351 0.811321
31 P5S 0.64557 0.826923
32 PEE 0.641026 0.796296
33 9PE 0.641026 0.811321
34 PEK 0.632184 0.830189
35 PC7 0.625 0.689655
36 LIO 0.625 0.689655
37 HGP 0.625 0.689655
38 6PL 0.625 0.689655
39 HGX 0.625 0.689655
40 PLD 0.625 0.689655
41 PX4 0.625 0.689655
42 PIE 0.613636 0.788462
43 6PH 0.608108 0.891304
44 F57 0.608108 0.891304
45 7PH 0.608108 0.891304
46 LPP 0.608108 0.891304
47 3PH 0.608108 0.891304
48 PX8 0.6 0.869565
49 PX2 0.6 0.869565
50 7P9 0.6 0.891304
51 S12 0.595238 0.826923
52 L9R 0.590909 0.666667
53 POV 0.590909 0.666667
54 EPH 0.589474 0.830189
55 MVC 0.589041 0.733333
56 OLB 0.589041 0.733333
57 OLC 0.589041 0.733333
58 PA8 0.586667 0.869565
59 AGA 0.585366 0.934783
60 XP5 0.580247 0.689655
61 PII 0.571429 0.823529
62 42H 0.569767 0.741379
63 CDL 0.567901 0.847826
64 PD7 0.56 0.891304
65 3TF 0.55914 0.618182
66 T7X 0.557895 0.843137
67 NKP 0.556962 0.913043
68 PSF 0.555556 0.826923
69 78M 0.554054 0.733333
70 78N 0.554054 0.733333
71 PIZ 0.550562 0.788462
72 PCK 0.549451 0.655738
73 1O2 0.548387 0.618182
74 TGL 0.542857 0.644444
75 M7U 0.542169 0.891304
76 PIF 0.54023 0.807692
77 IP9 0.539326 0.788462
78 HXG 0.536585 0.689655
79 PIO 0.522222 0.807692
80 52N 0.522222 0.807692
81 3PE 0.517647 0.735849
82 1EM 0.513514 0.688889
83 DGA 0.513514 0.688889
84 FAW 0.513514 0.688889
85 L2C 0.513514 0.688889
86 DDR 0.513514 0.688889
87 44E 0.513158 0.891304
88 DLP 0.510417 0.666667
89 1L2 0.504951 0.618182
90 MC3 0.488636 0.649123
91 PC1 0.488636 0.649123
92 PCF 0.488636 0.649123
93 PDK 0.485437 0.704918
94 BQ9 0.482759 0.711111
95 GGD 0.481132 0.625
96 LBR 0.469136 0.638298
97 1QW 0.465753 0.711111
98 GYM 0.465753 0.711111
99 LPC 0.465116 0.724138
100 LP3 0.465116 0.724138
101 LAP 0.465116 0.724138
102 PGM 0.457831 0.913043
103 NKN 0.443038 0.891304
104 NKO 0.443038 0.891304
105 SQD 0.43299 0.630769
106 G2A 0.430556 0.652174
107 2JT 0.430556 0.652174
108 CN5 0.426966 0.913043
109 DGD 0.421569 0.607143
110 OPC 0.405941 0.694915
Ligand no: 4; Ligand: CHD; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 CHD 1 1
2 GCH 0.785714 0.714286
3 DXC 0.609195 1
4 JN3 0.6 1
5 4OA 0.478261 0.972222
6 CHO 0.474747 0.714286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6JY3; Ligand: CHD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6jy3.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6jy3.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6jy3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6jy3.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6jy3.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: 1
This union binding pocket(no: 6) in the query (biounit: 6jy3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6A0S NDP 21.2766
Pocket No.: 7; Query (leader) PDB : 6JY3; Ligand: PEK; Similar sites found with APoc: 3
This union binding pocket(no: 7) in the query (biounit: 6jy3.bio1) has 97 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 12.3711
2 1NU4 MLA 12.3711
3 1NU4 MLA 12.3711
Pocket No.: 8; Query (leader) PDB : 6JY3; Ligand: PGV; Similar sites found with APoc: 3
This union binding pocket(no: 8) in the query (biounit: 6jy3.bio1) has 89 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 12.3711
2 1NU4 MLA 12.3711
3 1NU4 MLA 12.3711
Pocket No.: 9; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 6jy3.bio1) has 73 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 6jy3.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 6JY3; Ligand: PGV; Similar sites found with APoc: 3
This union binding pocket(no: 11) in the query (biounit: 6jy3.bio1) has 89 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA 12.3711
2 1NU4 MLA 12.3711
3 1NU4 MLA 12.3711
Pocket No.: 12; Query (leader) PDB : 6JY3; Ligand: CQX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 6jy3.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
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