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Receptor
PDB id Resolution Class Description Source Keywords
2WDQ 2.4 Å EC: 1.3.99.1 E. COLI SUCCINATE:QUINONE OXIDOREDUCTASE (SQR) WITH CARBOXIN BOUND ESCHERICHIA COLI SUCCINATE DEHYDROGENASE ACTIVITY CELL INNER MEMBRANE TRICAACID CYCLE CELL MEMBRANE METAL-BINDING TRANSMEMBRANE TRIRON-SULFUR FLAVOPROTEIN OXIDOREDUCTASE ELECTRON TRANSPOIRON HEME MEMBRANE
Ref.: STRUCTURE OF ESCHERICHIA COLI SUCCINATE:QUINONE OXIDOREDUCTASE WITH AN OCCUPIED AND EMPTY QUINONE-SITE. J.BIOL.CHEM. V. 284 29836 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CBE C:1130;
G:1130;
K:1130;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
235.302 C12 H13 N O2 S CC1=C...
F3S B:304;
F:304;
J:304;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
295.795 Fe3 S4 S1[Fe...
FAD A:601;
E:601;
I:601;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
FES B:302;
F:302;
J:302;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
175.82 Fe2 S2 S1[Fe...
HEM C:1129;
G:1129;
K:1129;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
NA A:1590;
E:1590;
I:1590;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
SF4 B:303;
F:303;
J:303;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
SO4 A:1591;
E:1591;
I:1591;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
TEO A:1589;
E:1589;
I:1589;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
132.072 C4 H4 O5 C(=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WDQ 2.4 Å EC: 1.3.99.1 E. COLI SUCCINATE:QUINONE OXIDOREDUCTASE (SQR) WITH CARBOXIN BOUND ESCHERICHIA COLI SUCCINATE DEHYDROGENASE ACTIVITY CELL INNER MEMBRANE TRICAACID CYCLE CELL MEMBRANE METAL-BINDING TRANSMEMBRANE TRIRON-SULFUR FLAVOPROTEIN OXIDOREDUCTASE ELECTRON TRANSPOIRON HEME MEMBRANE
Ref.: STRUCTURE OF ESCHERICHIA COLI SUCCINATE:QUINONE OXIDOREDUCTASE WITH AN OCCUPIED AND EMPTY QUINONE-SITE. J.BIOL.CHEM. V. 284 29836 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2WDQ - TEO C4 H4 O5 C(=C(O)/[O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2WDQ - TEO C4 H4 O5 C(=C(O)/[O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2WDQ - TEO C4 H4 O5 C(=C(O)/[O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CBE; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 CBE 1 1
Ligand no: 2; Ligand: TEO; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 TEO 1 1
2 TTN 0.409091 0.65
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WDQ; Ligand: CBE; Similar sites found with APoc: 60
This union binding pocket(no: 1) in the query (biounit: 2wdq.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4I54 1C1 3.7415
2 5B25 4QJ 3.87597
3 1ZDT PEF 5.21739
4 1OLM VTQ 5.21739
5 1BUC CAA 5.21739
6 4LSJ LSJ 5.42636
7 2JAQ DCP 5.42636
8 4POJ 2VP 6.08696
9 5AEE NSQ 6.30252
10 3Q9T FAY 6.95652
11 3FAL LO2 6.95652
12 1G94 DAF GLC DAF GLC GLC 6.97674
13 6ASY ATP 6.97674
14 5FMD NYT 6.97674
15 2I3G NAP 6.97674
16 6EOF ADP 6.97674
17 4WVO 3UZ 7.56302
18 4ZAH T5K 7.82609
19 3T58 FAD 7.98319
20 3LLI FAD 8.40336
21 1VL8 NAP 8.52713
22 1ZPD CIT 8.52713
23 3W54 RNB 8.69565
24 5X1M DHB 9.30233
25 5X1M THG 9.30233
26 4LOC OXM 9.30233
27 4DK7 0KS 9.66387
28 3UVD MB3 9.67742
29 2RDQ AKG 9.72222
30 2GJ5 VD3 10.0775
31 3WMX THR 10.084
32 5FBN 5WF 10.4348
33 5NNA BZM 10.4348
34 2E2R 2OH 10.5042
35 6HTO 5AD 10.8527
36 6HTO MET 10.8527
37 3KFC 61X 11.0672
38 4OKZ 3E9 11.3043
39 3QXQ CE5 11.3043
40 3CTY FAD 11.6279
41 1K6M AGS 11.6279
42 3QWB NDP 11.976
43 4KWD JF2 12.1019
44 4JEM C5P 12.3529
45 3DST GRG 12.4031
46 2XEM SSV 12.4031
47 3GPO APR 13.6905
48 2HZL PYR 14.7287
49 2IV3 UDP 14.7826
50 5K2M ADP 16.3866
51 4ZSY RW2 16.5217
52 6A56 LAT 16.5217
53 5ZCO TGL 17.8082
54 2R40 20E 18.0672
55 5XJ7 87O 20.8696
56 3V49 PK0 20.8696
57 6D6L FY4 20.9302
58 2UUU FAD 24.3478
59 2UUU PL3 24.3478
60 2BJ4 OHT 45.4545
Pocket No.: 2; Query (leader) PDB : 2WDQ; Ligand: TEO; Similar sites found with APoc: 79
This union binding pocket(no: 2) in the query (biounit: 2wdq.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZXM ANP 3.47826
2 2CWH NDP 3.79009
3 2CWH PYC 3.79009
4 2ZB3 NDP 4.24929
5 5NII FAD 4.34783
6 2YN4 39J 4.66102
7 1M5W DXP 4.93827
8 5W8Q BU4 5.42636
9 5E4R NAP 6.08696
10 5UWP GNP 6.20155
11 5DI9 GNP 6.20155
12 5UWS GNP 6.20155
13 2WME NAP 6.20155
14 2Z48 NGA 6.94444
15 2Z49 AMG 6.94444
16 2X06 NAD 6.95652
17 3WBF API 7.14286
18 5UIJ TYD 7.82609
19 3RS8 APR 7.82609
20 3VC3 C6P 7.82609
21 3LF0 ATP 7.89474
22 3KV8 FAH 7.91367
23 5DNK SAH 8.40336
24 1GPM AMP 8.52713
25 4XDA ADP 8.69565
26 4C5N ACP 8.82353
27 4K49 HFQ 9.56522
28 5WYZ 7VF 9.66387
29 5N9Z CAP 10.0775
30 4LXQ TYD 10.084
31 4LXQ FON 10.084
32 6G9I CXX 10.119
33 1OFU GDP 10.3125
34 4QIJ 1HA 10.4348
35 3WYF GTP 10.4348
36 1J0D 5PA 10.4348
37 5DX0 SFG 10.4348
38 5DWQ SFG 10.4348
39 4OBW SAM 10.5058
40 1V9N NDP 10.8527
41 2YPI PGA 10.8527
42 1EZ0 NAP 11.3043
43 1IG3 VIB 11.6279
44 4R3U 3KK 11.6279
45 4Y4V DAL 12.1739
46 3NW7 LGV 12.4031
47 4R6W SAH 12.4031
48 2XVM SAH 12.5628
49 4CBX ATP 12.5984
50 1YAG ATP 12.8
51 3H86 AP5 13.9535
52 1R37 NAD 14.7287
53 2FXU BID 15.5039
54 1KXP ATP 15.5039
55 3MN9 ATP 15.5039
56 3MN7 ATP 15.5039
57 3MN6 ATP 15.5039
58 4PL8 ATP 15.5039
59 4B1W ATP 15.5039
60 1SQK ADP 15.5039
61 2V51 ATP 15.5039
62 4IZC 1GZ 15.6364
63 2JC9 ADN 15.6522
64 1FFU FAD 15.9509
65 2PBD ATP 16.2791
66 4QYS PLP SEP 16.5217
67 3OVR 5SP 17.9825
68 2FF3 ATP 18
69 1RM6 FAD 18.0124
70 5EYP GTP 18.6047
71 5HTL C2E 25.5172
72 2A3Z ATP 26.087
73 2A40 ATP 26.087
74 2D1K ATP 26.087
75 2A42 ATP 26.087
76 5DXA SFG 26.3158
77 5ZYN SIN 32.6531
78 4B1V LAB 46.875
79 4B1V ATP 46.875
Pocket No.: 3; Query (leader) PDB : 2WDQ; Ligand: CBE; Similar sites found with APoc: 22
This union binding pocket(no: 3) in the query (biounit: 2wdq.bio3) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4B9Q ATP 5.21739
2 3R35 4CO 5.96026
3 4M8E 29V 6.08696
4 4AQL TXC 6.95652
5 4L80 1VU 7.56302
6 1CJW COT 7.82609
7 3EM0 CHD 7.97101
8 4D1J DGJ 9.30233
9 1MO9 KPC 10.0775
10 1MO9 FAD 10.0775
11 5A86 D7E 10.1911
12 4LA7 A1O 12.4031
13 4LZJ 22H 12.4031
14 2ZRU FMN 13.0435
15 3AB4 THR 13.4831
16 3OKI OKI 13.913
17 3B12 FAH 13.9535
18 3L0E G58 14.7059
19 1T26 GBD 15.5039
20 1T26 NAI 15.5039
21 1SR7 MOF 17.2269
22 3IPQ 965 32
Pocket No.: 4; Query (leader) PDB : 2WDQ; Ligand: TEO; Similar sites found with APoc: 27
This union binding pocket(no: 4) in the query (biounit: 2wdq.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 5F90 GLA GAL 4.65116
2 1QZR ANP 5.04202
3 2Y6Q I7T 6.20155
4 2Y6Q FAD 6.20155
5 5H4S RAM 6.30252
6 3W9Z FMN 7.14286
7 3T7S SAM 7.75194
8 2TPS TPS 9.56522
9 4CZG ADP 10.4348
10 4CZG QH3 10.4348
11 4EFH ADP 11.3043
12 4GJ3 0XP 11.6279
13 3NUG NAD 11.6279
14 1V3S ATP 12.931
15 3SJH ATP 15.5039
16 4PKG ATP 15.5039
17 3U9Z ADP 15.5039
18 3SJH LAR 15.5039
19 5YEE ATP 15.5039
20 4PKI ATP 15.5039
21 2FF6 ATP 18
22 4B1X ATP 18.75
23 3WYG GTP 22.3684
24 3MN5 ATP 23.2558
25 5ZZB ATP 23.2558
26 2PAV ATP 25
27 5ZYN FAD 32.6531
Pocket No.: 5; Query (leader) PDB : 2WDQ; Ligand: TEO; Similar sites found with APoc: 12
This union binding pocket(no: 5) in the query (biounit: 2wdq.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z48 A2G 6.94444
2 2ART LPA AMP 8.01527
3 1ON3 MCA 9.30233
4 4UTG ANP 10.4348
5 1LLU NAD 10.5263
6 3OFK SAH 11.3043
7 4XDY NAI 12.1739
8 6B3V ANP 13.1783
9 4YGM URA 13.1783
10 2O66 FLC 14.0741
11 3FSY SCA 14.7826
12 1IR2 CAP 19.1304
Pocket No.: 6; Query (leader) PDB : 2WDQ; Ligand: CBE; Similar sites found with APoc: 36
This union binding pocket(no: 6) in the query (biounit: 2wdq.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1YP0 PEF 4.62185
2 4D7E FAD 4.65116
3 5Y02 HBX 5.60748
4 6ALW BNV 6.08696
5 2C5S AMP 6.08696
6 3U2U UDP 6.08696
7 6EJI UD2 6.20155
8 3I54 CMP 6.20155
9 5O4J PJL 6.20438
10 5O4J SAH 6.20438
11 5O4J 9KH 6.20438
12 4XBA GMP 6.5
13 3PTQ NFG 6.73267
14 3GXO MQA 6.97674
15 4OMJ 2TX 7.19424
16 6CD1 PLG 7.75194
17 6CD1 PLS 7.75194
18 1I58 ADP 8.46561
19 3FQ8 PMP 8.52713
20 1GQG DCD 9.30233
21 4G5H NAP 10.1928
22 4G5H UD7 10.1928
23 5DJU FMN 10.3448
24 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 11.3043
25 5XWV 8H6 11.6279
26 4L77 CNL 12.1739
27 4P42 PEE 12.605
28 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 13
29 1YQD NAP 13.1148
30 3RGA ILD 13.4454
31 2DTJ THR 13.4831
32 1W5T ADP 14.7826
33 2I7N ACO 17.8295
34 3OJF NDP 18.2609
35 5OE4 3UK 19.1304
36 2IYG FMN 21.7742
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