Receptor
PDB id Resolution Class Description Source Keywords
2Y69 1.95 Å EC: 1.9.3.1 BOVINE HEART CYTOCHROME C OXIDASE RE-REFINED WITH MOLECULAR OXYGEN BOS TAURUS ELECTRON TRANSPORT COMPLEX IV PROTON PUMPS MEMBRANE PROTE
Ref.: A COMBINED QUANTUM CHEMICAL AND CRYSTALLOGRAPHIC ST THE OXIDIZED BINUCLEAR CENTER OF CYTOCHROME C OXIDA BIOCHIM.BIOPHYS.ACTA V.1807 769 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CHD A:1517;
C:1265;
G:1085;
N:1517;
P:1265;
T:1085;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
408.571 C24 H40 O5 C[C@H...
CU A:517;
N:517;
Part of Protein;
Part of Protein;
none;
none;
submit data
63.546 Cu [Cu+2...
CUA B:228;
O:228;
Part of Protein;
Part of Protein;
none;
none;
submit data
127.092 Cu2 [Cu][...
DMU M:1044;
Z:1043;
Invalid;
Invalid;
none;
none;
submit data
482.562 C22 H42 O11 CCCCC...
HEA A:515;
A:516;
N:515;
N:516;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
852.837 C49 H56 Fe N4 O6 Cc1c2...
MG A:1516;
N:1516;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
OXY A:1515;
N:1515;
Invalid;
Invalid;
none;
none;
submit data
31.999 O2 O=O
PEK C:1262;
P:1262;
Invalid;
Invalid;
none;
none;
submit data
768.055 C43 H78 N O8 P CCCCC...
PGV C:1263;
C:1264;
P:1263;
P:1264;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
749.007 C40 H77 O10 P CCCCC...
ZN F:1097;
S:1097;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Y69 1.95 Å EC: 1.9.3.1 BOVINE HEART CYTOCHROME C OXIDASE RE-REFINED WITH MOLECULAR OXYGEN BOS TAURUS ELECTRON TRANSPORT COMPLEX IV PROTON PUMPS MEMBRANE PROTE
Ref.: A COMBINED QUANTUM CHEMICAL AND CRYSTALLOGRAPHIC ST THE OXIDIZED BINUCLEAR CENTER OF CYTOCHROME C OXIDA BIOCHIM.BIOPHYS.ACTA V.1807 769 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2Y69 - CHD C24 H40 O5 C[C@H](CCC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2Y69 - CHD C24 H40 O5 C[C@H](CCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5WAU - CHD C24 H40 O5 C[C@H](CCC....
2 5W97 - CHD C24 H40 O5 C[C@H](CCC....
3 2Y69 - CHD C24 H40 O5 C[C@H](CCC....
Polypharmacology
Similar Ligands
Ligand no: 1; 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 : 2Y69; Ligand: CHD; Similar sites found: 112
This union binding pocket(no: 1) in the query (biounit: 2y69.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3SE5 ANP 0.02224 0.40281 7.31707
2 2QZT PLM 0.01194 0.43088 7.93651
3 2XSU PIE 0.02581 0.41528 7.93651
4 4RHP PEF 0.006057 0.42999 8.75
5 3GWT 066 0.02071 0.42326 8.81226
6 3OV6 MK0 0.02169 0.42165 10
7 4I4B 1CV 0.04542 0.40007 10
8 3WHB DCC 0.03879 0.41317 10.4651
9 1DEK DGP 0.02416 0.40361 10.4651
10 4H6Q TFB 0.01363 0.42471 11.1111
11 2EW5 Y12 0.01445 0.41467 11.1111
12 3G08 FEE 0.03037 0.42861 11.25
13 4RW3 TDA 0.003608 0.43406 11.6279
14 3MAX LLX 0.03107 0.40831 11.6279
15 1M5W DXP 0.03028 0.40992 11.8421
16 5GK9 ACO 0.005402 0.4494 12
17 4Q9M FPP 0.03201 0.41221 12.1622
18 3G58 988 0.01158 0.41167 12.1622
19 5IF4 6AK 0.02803 0.41224 12.5
20 3G4G D71 0.003466 0.45006 12.7753
21 3QKD HI0 0.01706 0.41831 12.7907
22 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.02779 0.40917 12.7907
23 1U1B PAX 0.03623 0.41235 12.9032
24 2GJ3 FAD 0.02645 0.40156 13.3333
25 1EU8 TRE 0.01816 0.41407 13.5135
26 2A14 SAH 0.0309 0.40289 13.75
27 1XMY ROL 0.009604 0.41374 13.8158
28 1XMU ROF 0.01674 0.4082 13.8158
29 1ZMD FAD 0.03788 0.41499 13.9535
30 2F5Z FAD 0.04003 0.41369 13.9535
31 4B5P ACO 0.001432 0.48188 14.2012
32 3G5K BB2 0.009885 0.41938 14.2012
33 3KXC PLM 0.01773 0.41703 14.2857
34 1S17 GNR 0.01577 0.41221 14.2857
35 5CHR 4NC 0.01231 0.40356 14.2857
36 4DXJ 0M9 0.04286 0.4023 14.2857
37 4DXJ IPE 0.04698 0.4023 14.2857
38 4ITU NAI 0.01718 0.4244 14.433
39 1Q6O LG6 0.02163 0.40032 14.433
40 2OI9 GLN LEU SER PRO PHE PRO PHE ASP LEU 0.01074 0.45337 14.5251
41 3BXF 13P 0.01835 0.40897 15
42 2WPW ACO 0.02417 0.40101 15
43 2PX6 DH9 0.01532 0.40943 15.4639
44 4JHG ZEA 0.01223 0.41165 15.7143
45 2YLD CMO 0.006429 0.41736 15.748
46 3E7O 35F 0.009351 0.44416 16.25
47 1U8V FAD 0.04825 0.40421 16.4474
48 2VBQ BSJ 0.01135 0.44168 17.0543
49 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.0475 0.41246 17.2414
50 1UCD URA 0.01584 0.41536 17.4419
51 5CSD ACD 0.04358 0.40745 17.4603
52 4H6U ACO 0.004302 0.44692 17.5
53 3E8T UQ8 0.04631 0.42127 17.5
54 3ORF NAD 0.04746 0.40005 17.5
55 3NTD COA 0.03991 0.40963 17.7632
56 1M13 HYF 0.01171 0.43758 18.3432
57 1KQN NAD 0.04359 0.40638 18.5567
58 3HUJ AGH 0.02662 0.42802 18.6047
59 5BYZ 4WE 0.02668 0.41317 18.6047
60 5V2J UDP 0.03388 0.40946 18.6047
61 5V2J 7WV 0.03297 0.40907 18.6047
62 1BWO LPC 0.01512 0.4157 18.75
63 5B4B LP5 0.03607 0.40865 18.75
64 3PMD 11A 0.0154 0.40303 18.75
65 5UI2 EQ3 0.04609 0.40774 19.0476
66 3L9R L9R 0.01715 0.42411 19.3878
67 4DV8 0LX 0.02319 0.42338 19.7674
68 3SCM LGN 0.04549 0.41821 19.7674
69 1OW4 2AN 0.01166 0.41557 20
70 2CNT COA 0.0175 0.41134 20
71 2WH8 II2 0.008666 0.41041 20.2703
72 1RQJ RIS 0.03262 0.40176 20.2703
73 2J8C U10 0.04771 0.42382 20.6349
74 2J8C SPO 0.04771 0.42382 20.6349
75 4DR9 BB2 0.01178 0.41489 20.6349
76 3T6E UQ9 0.01836 0.4315 21.25
77 1TFZ 869 0.02872 0.40213 21.6495
78 3SVJ 4LI 0.01193 0.41963 21.7054
79 4IEH 1E9 0.0192 0.41432 21.8935
80 3U2U UDP 0.02486 0.41954 22.5
81 4M8E 29V 0.00479 0.4503 22.8571
82 3H0A D30 0.01202 0.42876 22.8571
83 3H0A 9RA 0.008973 0.42844 22.8571
84 3FAL REA 0.01236 0.41837 22.8571
85 1FBY REA 0.02255 0.41597 22.8571
86 2YYJ FAD 0.006986 0.45317 22.973
87 3K9U ACO 0.03132 0.42827 23.0263
88 1EE0 CAA 0.01539 0.4249 23.0769
89 3O26 NDP 0.03483 0.40423 23.6686
90 1EM6 CP4 0.02608 0.45448 23.7113
91 2Y31 SMQ 0.02867 0.41417 23.8095
92 1UVC STE 0.02854 0.41094 24.1758
93 1T90 NAD 0.03703 0.40953 24.3243
94 2FDW D3G 0.006946 0.42193 25.6757
95 3KEE 30B 0.0303 0.40243 26.087
96 4WO4 JLS 0.01443 0.43948 26.25
97 4NKW PLO 0.02347 0.40062 26.3158
98 3EXS 5RP 0.01163 0.41088 26.7442
99 2XAU ADP 0.01967 0.40324 26.7442
100 1W96 S1A 0.02024 0.40765 26.9841
101 2YOO K2B 0.01704 0.41425 27.1429
102 3STD MQ0 0.02873 0.40127 27.907
103 2ALG HP6 0.007064 0.43337 28.2609
104 2ALG DAO 0.007064 0.43337 28.2609
105 1Q1Y BB2 0.007098 0.42453 28.3784
106 1Y0G 8PP 0.03405 0.42194 29.7297
107 3ANP DCC 0.04484 0.40199 30
108 1KDO C 0.02966 0.40084 31.4286
109 2A1L PCW 0.02307 0.43021 32.5
110 2GU8 796 0.02955 0.43175 35
111 2R40 EPH 0.009789 0.43439 36.25
112 2OKL BB2 0.01056 0.41906 36.5079
Pocket No.: 2; Query (leader) PDB : 2Y69; Ligand: CHD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2y69.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2Y69; Ligand: CHD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2y69.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2Y69; Ligand: CHD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2y69.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2Y69; Ligand: CHD; Similar sites found: 68
This union binding pocket(no: 5) in the query (biounit: 2y69.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TIQ COA 0.01195 0.41799 6.57895
2 4XB4 45D 0.04034 0.41105 8.13953
3 3E85 BSU 0.02869 0.4209 8.24742
4 3JUQ AJD 0.01142 0.42612 9.30233
5 3JUQ AKD 0.01218 0.42612 9.30233
6 3ET1 ET1 0.0192 0.41233 10.3093
7 5FH7 5XL 0.01239 0.41598 10.8108
8 2OBD PCW 0.04131 0.40576 11.4286
9 3TDV GDP 0.004371 0.43686 11.6279
10 4OMJ 2TX 0.04919 0.40136 11.6279
11 3NT6 FAD 0.0469 0.40892 11.8421
12 3NT6 COA 0.03855 0.40694 11.8421
13 4Q9M 2ZW 0.02243 0.40122 12.1622
14 1O6U PLM 0.02473 0.40134 12.5
15 2HPL ASP ASP LEU TYR GLY 0.004797 0.42269 12.8571
16 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.006124 0.41224 12.8571
17 1HK8 DGT 0.03335 0.40237 12.8571
18 5LJ0 6XX 0.02744 0.41353 13.0769
19 1ZDT PEF 0.01141 0.42762 13.9535
20 2FT0 ACO 0.009245 0.41812 14.2857
21 1K7L 544 0.04366 0.40217 14.2857
22 4WN5 MVC 0.02752 0.4105 14.7826
23 5MES 7LT 0.01388 0.40678 15
24 4AT0 FAD 0.02454 0.43575 15.7143
25 3GFZ FMN 0.01962 0.40754 15.873
26 5U98 1KX 0.03123 0.42769 16.1616
27 3Q8G PEE 0.04099 0.4221 16.25
28 2X5W K2B 0.02844 0.40568 16.25
29 3OGN 3OG 0.02717 0.40144 16.25
30 1N8V BDD 0.0213 0.40063 16.4948
31 3CV3 UDP 0.01894 0.40066 17.1429
32 4KVX ACO 0.008479 0.43105 17.5676
33 1XAP TTB 0.02762 0.40885 18.5567
34 5C9J STE 0.00588 0.43611 18.5714
35 2Q4G CIT 0.0139 0.40452 18.5714
36 4YC9 4C1 0.01319 0.4138 18.6047
37 1TV5 N8E 0.011 0.40368 18.9189
38 3L9R L9Q 0.01545 0.4194 19.3878
39 2ZW5 COA 0.02355 0.40206 19.7674
40 5KOR GDP 0.02492 0.40121 20
41 1GHE ACO 0.007128 0.43683 20.6186
42 2B4D COA 0.01098 0.42696 20.6349
43 2Q2V NAD 0.03753 0.40398 20.6349
44 2ZPA ACO 0.02486 0.41486 21.25
45 3GGO NAI 0.03831 0.41247 21.25
46 3GGO ENO 0.03831 0.41247 21.25
47 3ZM6 2GN 0.02842 0.40735 21.4286
48 5CUQ NSC 0.01019 0.44735 21.6216
49 5FUE UV4 0.01937 0.40492 21.6495
50 1X0P FAD 0.02572 0.40132 21.6783
51 1SOX MTE 0.02374 0.40873 22.5
52 3RUG DB6 0.04364 0.41047 22.973
53 1RDT L79 0.007789 0.43565 24
54 3BEJ MUF 0.04041 0.40092 24
55 3W68 VIV 0.01626 0.40922 24.2857
56 3VPH NAD 0.0432 0.40613 24.3243
57 3JYN NDP 0.01857 0.42197 25.3968
58 1SQ5 ADP 0.01797 0.4039 25.3968
59 4LOK 1YD 0.04186 0.41077 26.9841
60 4NZ4 NDG 0.0235 0.40568 26.9841
61 2AX9 BHM 0.03358 0.41283 27.1429
62 3OLL EST 0.01796 0.40534 27.1429
63 1O94 ADP 0.02477 0.4123 27.5
64 2FYU FDN 0.0159 0.41307 28.5714
65 4DVQ 1CA 0.01516 0.4018 28.75
66 2C3Q GTX 0.01594 0.40999 33.75
67 1NUS APC 0.02678 0.42243 34.0206
68 4V3I ASP LEU THR ARG PRO 0.011 0.40095 36.5079
Pocket No.: 6; Query (leader) PDB : 2Y69; Ligand: CHD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2y69.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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