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Receptor
PDB id Resolution Class Description Source Keywords
5AEW 1.88 Å EC: 1.14.12.18 CRYSTAL STRUCTURE OF II9 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 IN COMPLEX WITH B IPHENYL BURKHOLDERIA XENOVORANS LB400 OXIDOREDUCTASE BIPHENYL DIOXYGENASE BPHAE-II9 BIPHENYL POLYCHLORINATED BIPHENYLS
Ref.: STRUCTURAL BASIS OF THE ENHANCED POLLUTANT-DEGRADIN CAPABILITIES OF AN ENGINEERED BIPHENYL DIOXYGENASE. J.BACTERIOL. V. 198 1499 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FES O:460;
Q:460;
G:460;
A:460;
U:460;
E:460;
M:460;
W:460;
S:460;
C:460;
K:460;
I:460;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
175.82 Fe2 S2 S1[Fe...
BNL I:462;
S:462;
C:462;
Q:462;
O:462;
K:462;
M:462;
W:462;
E:462;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
154.208 C12 H10 c1ccc...
FE2 C:461;
A:461;
S:461;
W:461;
E:461;
Q:461;
O:461;
M:461;
K:461;
U:461;
G:461;
I:461;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
55.845 Fe [Fe+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5AEW 1.88 Å EC: 1.14.12.18 CRYSTAL STRUCTURE OF II9 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 IN COMPLEX WITH B IPHENYL BURKHOLDERIA XENOVORANS LB400 OXIDOREDUCTASE BIPHENYL DIOXYGENASE BPHAE-II9 BIPHENYL POLYCHLORINATED BIPHENYLS
Ref.: STRUCTURAL BASIS OF THE ENHANCED POLLUTANT-DEGRADIN CAPABILITIES OF AN ENGINEERED BIPHENYL DIOXYGENASE. J.BACTERIOL. V. 198 1499 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5AEW - BNL C12 H10 c1ccc(cc1)....
2 2XSH - DC5 C12 H8 Cl2 c1ccc(cc1)....
3 2YFJ - 1IT C12 H8 O c1ccc2c(c1....
4 2XRX - BNL C12 H10 c1ccc(cc1)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5AEW - BNL C12 H10 c1ccc(cc1)....
2 2XSH - DC5 C12 H8 Cl2 c1ccc(cc1)....
3 2YFJ - 1IT C12 H8 O c1ccc2c(c1....
4 2XRX - BNL C12 H10 c1ccc(cc1)....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5AEW - BNL C12 H10 c1ccc(cc1)....
2 2XSH - DC5 C12 H8 Cl2 c1ccc(cc1)....
3 2YFJ - 1IT C12 H8 O c1ccc2c(c1....
4 2XRX - BNL C12 H10 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BNL; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BNL 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 45
This union binding pocket(no: 1) in the query (biounit: 5aew.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4LZJ 22H 1.65016
2 5LI1 ANP 2.65957
3 5UIU 8CG 3.19149
4 6AM8 PLT 3.19149
5 1VJ7 GPX 3.30789
6 4BFM ANP 3.7234
7 5OC1 ANN 3.7234
8 1XDY MTE 4.02685
9 5L4S NAP 4.25532
10 5L4S 6KX 4.25532
11 1T7Q COA 4.3573
12 1T7Q 152 4.3573
13 4MPO AMP 4.57516
14 6CEP NAD 4.78723
15 6CEP OXM 4.78723
16 3RUV ANP 5.31915
17 5UR1 YY9 5.31915
18 5IXG OTP 5.32544
19 2B9H ADP 5.38244
20 2B9J ADP 5.38244
21 1LLU NAD 5.85106
22 3H7J PPY 5.85106
23 1JBW ACQ 6.38298
24 4D1J DGJ 6.38298
25 1SW1 PBE 6.54545
26 6F3M NAD 6.91489
27 5YRG BGC GLC 7.04225
28 5YRJ BGC GLC 7.04225
29 5YRM BGC GLC 7.04225
30 1Z03 OCH 7.17489
31 5AWQ GLC GLC 7.44681
32 6CUZ FEV 7.73196
33 1UUO BRF 8.51064
34 2RKV ZBA 8.64745
35 2CI5 HCS 9.15493
36 5YXC CIT 9.25926
37 3RV5 DXC 10.1124
38 1VQ2 DDN 11.399
39 1Q3Q ANP 11.7021
40 4YZN 4K5 12.234
41 4IDT T28 15.4255
42 3VMG 9CA 19.1304
43 3KO0 TFP 21.7822
44 2CNE DFJ 23.4043
45 2BMR 3NT 47.4273
Pocket No.: 2; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 30
This union binding pocket(no: 2) in the query (biounit: 5aew.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3QCJ NX4 2.12766
2 2O1S TDP 2.17865
3 2I0K FAD 3.19149
4 3RI1 3RH 3.19149
5 4Z87 5GP 3.7234
6 4Z0G 5GP 3.7234
7 5XDT MB3 3.7234
8 1UXG NAD 4.20712
9 1UXG FUM 4.20712
10 3C9U TPP 4.25532
11 3C9U ADP 4.25532
12 4UX9 ANP 4.3956
13 4WNP 3RJ 4.78723
14 4B7S QLE 5.31915
15 4UDB CV7 5.85106
16 4OYA 1VE 6.38298
17 4AR8 IP8 GLY PRO ALA 6.38298
18 1Z0N BCD 8.33333
19 5A5W GUO 8.51064
20 6CMJ F6J 9.57447
21 1SIV PSI 10.101
22 6C7Y ADP 12.2378
23 5T8O 76Z 14.3617
24 5UKL SIX 14.7493
25 1R37 ETX 15.562
26 1V0O INR 17.0139
27 2Z3U CRR 20.7447
28 4C2V YJA 25
29 4X9D U5P 30.9859
30 3E5A VX6 34.0909
Pocket No.: 3; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5aew.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2GTE VA 2.41935
2 5JZJ AN2 3.19149
3 1U7T TDT 5.85106
4 4OTH DRN 9.97067
5 2PVN P63 10.6383
6 4A34 FUL 10.8844
7 4UIB GWX 11.7021
8 1V8B NAD 12.766
Pocket No.: 4; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 54
This union binding pocket(no: 4) in the query (biounit: 5aew.bio4) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1KYZ FER 2.12766
2 4ZAH T5K 2.27273
3 2FK8 SAM 2.65957
4 4A6D SAM 2.65957
5 1DRY AKG 2.65957
6 1DRY AAG 2.65957
7 2XK9 XK9 3.19149
8 4H3Q ANP 3.19149
9 6D55 FWA 3.19149
10 1TPY SAH 3.48432
11 3LXK MI1 3.7234
12 2WLG SOP 4.18605
13 3ATY FMN 4.25532
14 1KPH SAH 4.25532
15 2Q1W NAD 4.25532
16 1KPG SAH 4.25532
17 6BWL NAD 4.57317
18 1ICV FMN 4.78723
19 4EWH T77 5.09091
20 2PI8 NAG NAG NAG NAG NAG NAG 5.31915
21 3PNL ADP 5.31915
22 2Q3R FMN 5.31915
23 1P6D 3PC 5.31915
24 3SFI 3SF 5.85106
25 4ELG 52J 6.0241
26 1U1I NAD 6.12245
27 1LQA NDP 6.38298
28 2XTS MTE 6.38298
29 3SJU NDP 6.45161
30 3WBF API 6.55738
31 3DUV KDO 6.87023
32 4UWJ 7L5 6.91489
33 4UWJ MYA 6.91489
34 2O07 MTA 6.91489
35 2O07 SPD 6.91489
36 1RM6 FAD 6.91489
37 5GM1 SAH 7.07071
38 2VL1 GLY GLY 7.44681
39 5ZAI COA 7.44681
40 2Y3S TIR 7.97872
41 4YDQ HFG 8.51064
42 4YDQ ANP 8.51064
43 3TTC ADP 8.51064
44 1GT4 UNA 8.80503
45 2GZ3 NAP 10.1064
46 5L9G MO0 10.6383
47 2H04 4UN 11.1702
48 1FFU CDP 11.6564
49 6GU6 1QK 12.234
50 3EI9 PL6 12.766
51 2D0V PQQ 15.2778
52 6C6O ENG 15.9574
53 4AZJ SEP PLP 16.4894
54 1N62 MCN 18.0851
Pocket No.: 5; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 25
This union binding pocket(no: 5) in the query (biounit: 5aew.bio4) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3RUU 37G 2.62009
2 2BEK ATP 3.11284
3 3WRB GDE 3.7234
4 4Q9M FPP 4.47154
5 5X2Z 3LM 4.78723
6 1P7L ANP 4.78723
7 1P7L MET 4.78723
8 6A5Y 9R0 5.04202
9 4ZUL UN1 5.85106
10 4L80 1VU 5.85106
11 5W19 9TD 7.97872
12 6CDG PRO GLY LEU TRP LYS SER 8.38323
13 4QDC ASD 8.71795
14 1DUB CAA 9.04255
15 1UU1 PMP HSA 9.04255
16 1QXW M1C 9.04255
17 1V97 MTE 10.6383
18 3JZB 4HY 11.7021
19 3DLS ADP 13.2979
20 2VE3 REA 13.8298
21 1C9H RAP 14.0187
22 4UP4 NDG 14.3617
23 4UP4 NAG 14.3617
24 3DCJ THH 15.9574
25 4OFG PCG 28.4722
Pocket No.: 6; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 41
This union binding pocket(no: 6) in the query (biounit: 5aew.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3EAU PDN 1.52905
2 3EAU NDP 1.52905
3 3TKY SAH 3.19149
4 3IU9 T07 3.47222
5 6H3O FAD 3.7234
6 3AYS CT3 4.25532
7 2BZG SAH 4.74138
8 5K8S CMP 6.08108
9 1RP7 TZD 6.10022
10 5KBF CMP 6.31229
11 2ZI8 SDT 6.66667
12 6CDO ALA VAL GLY ILE GLY ALA VAL PHE 6.84932
13 3KV8 FAH 7.19424
14 5EIN NAP 7.40741
15 6A1G 9OL 7.44681
16 3F3E LEU 7.44681
17 5DEP UD1 7.44681
18 4MA6 28E 7.64331
19 4H2W 5GP 7.80347
20 5YSZ CBI 7.97872
21 1PJ6 FOL 8.51064
22 3WV1 WHH 8.77193
23 2V7O DRN 8.92857
24 6B5Q PPI CZS 2KY MLY 1XY 9.04255
25 4BXK 1IU 9.57447
26 5N8V KZZ 10.1449
27 1Q3A NGH 12.1212
28 2I3G NAP 12.234
29 3ZBQ GDP 12.234
30 2WU6 DKI 12.5984
31 1YRX FMN 13.2231
32 4EJ1 FOL 14.9254
33 4WZV E40 16.25
34 2FKW RG1 17.0732
35 4QWT ACD 17.5532
36 5ZCO PGV 17.8082
37 2DYR PGV 17.8082
38 5Z84 PGV 17.8082
39 2DYS PGV 17.8082
40 3VPB ADP 29.7872
41 3VPC ADP 29.7872
Pocket No.: 7; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 11
This union binding pocket(no: 7) in the query (biounit: 5aew.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1FP1 SAH 2.12766
2 6BA2 7KM 5.31915
3 1IDA 0PO 6.06061
4 5JE0 AZ8 6.38298
5 5JE0 SAH 6.38298
6 6C3C EJ1 7.44681
7 3AHC TPP 9.04255
8 6D6L FY4 10
9 1N46 PFA 10.6383
10 1EU8 TRE 14.8936
11 2Y88 2ER 19.1489
Pocket No.: 8; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 7
This union binding pocket(no: 8) in the query (biounit: 5aew.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1JG3 ADN 2.12766
2 4UAL 3FV 3.10263
3 6D5V FVY 3.19149
4 4B7P 9UN 7.44681
5 2VAR KDF 9.04255
6 2VAR KDG 9.04255
7 1U6R IOM 15.4255
Pocket No.: 9; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 7
This union binding pocket(no: 9) in the query (biounit: 5aew.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3AY6 BGC 2.23048
2 4WGF HX2 3.7234
3 3CQO FUC 5.80205
4 1PVN MZP 7.44681
5 3B8X G4M 7.97872
6 6BXI ANP 9.04255
7 5B48 TDN 13.4426
Pocket No.: 10; Query (leader) PDB : 5AEW; Ligand: BNL; 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: 5aew.bio5) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5AEW; Ligand: BNL; Similar sites found with APoc: 1
This union binding pocket(no: 11) in the query (biounit: 5aew.bio5) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1IIU RTL 21.2644
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