Receptor
PDB id Resolution Class Description Source Keywords
5X1N 2 Å EC: 7.-.-.- VANILLATE/3-O-METHYLGALLATE O-DEMETHYLASE, LIGM, PROTOCATECH TETRAHYDROFOLATE COMPLEX FORM SPHINGOBIUM SP. SYK-6 LIGNIN SPHINGOBIUM SP. SYK-6 OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF A NEW O-DEMETHYLASE FROM SPHINGOBIUM SP. STRAIN SYK-6 FEBS J. V. 284 1855 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
THG A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
445.429 C19 H23 N7 O6 c1cc(...
EDO B:504;
A:503;
A:504;
B:503;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
DHB B:502;
A:502;
Valid;
Valid;
none;
none;
submit data
154.12 C7 H6 O4 c1cc(...
TRS A:505;
B:505;
Invalid;
Invalid;
none;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X1M 1.9 Å EC: 7.-.-.- VANILLATE/3-O-METHYLGALLATE O-DEMETHYLASE, LIGM, PROTOCATECH TETRAHYDROFOLATE COMPLEX FORM SPHINGOBIUM SP. SYK-6 LIGNIN SPHINGOBIUM SP. SYK-6 OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF A NEW O-DEMETHYLASE FROM SPHINGOBIUM SP. STRAIN SYK-6 FEBS J. V. 284 1855 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5X1L - THG C19 H23 N7 O6 c1cc(ccc1C....
2 5X1J - VNL C8 H7 O4 COc1cc(ccc....
3 5X1K - 7WR C8 H8 O5 COc1cc(cc(....
4 5X1N - DHB C7 H6 O4 c1cc(c(cc1....
5 5X1M - DHB C7 H6 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: THG; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 THG 1 1
2 1YJ 1 1
3 1YA 0.66 0.954545
4 C2F 0.623762 0.887324
5 FFO 0.617647 0.926471
6 FON 0.518182 0.926471
7 THF 0.490909 0.873239
8 9L9 0.484848 0.892308
9 TLL 0.478632 0.863014
10 MEF 0.469027 0.84
11 DHF 0.462963 1
12 THH 0.455357 0.733333
13 GHC 0.454545 0.684211
14 3TZ 0.452174 0.774648
15 29C 0.452174 0.838235
16 29D 0.452174 0.838235
17 28Z 0.452174 0.838235
18 83A 0.45045 0.826087
19 GHW 0.449541 0.693333
20 FOL 0.428571 0.863636
21 DZF 0.428571 0.848485
22 LYA 0.422018 0.782609
23 DXZ 0.401786 0.777778
24 DXY 0.401786 0.777778
25 21V 0.4 0.910448
26 DDF 0.4 0.910448
Ligand no: 2; Ligand: DHB; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 DHB 1 1
2 FHB 0.514286 0.72
3 4A3 0.514286 0.655172
4 IHB 0.514286 0.72
5 CHB 0.514286 0.72
6 3HB 0.428571 0.761905
7 GDE 0.424242 0.913043
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found: 50
This union binding pocket(no: 1) in the query (biounit: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M0T AKG 0.04595 0.40238 1.70068
2 5HTX ADP 0.02123 0.41052 1.82232
3 5IFK HPA 0.04279 0.40558 1.92308
4 5KJW 53C 0.03856 0.40557 2.10773
5 3GXO MQA 0.03248 0.40481 2.43902
6 4CJN QNZ 0.002019 0.47605 2.53165
7 5FAW CHT 0.02831 0.41201 2.53165
8 5E58 CPZ 0.03356 0.40514 2.74262
9 4WVW SLT 0.01817 0.41488 2.77778
10 3WGC PLG 0.01256 0.41082 2.93255
11 3HQP OXL 0.02385 0.41047 2.95359
12 4XBA 5GP 0.01821 0.40655 3
13 4LH7 NMN 0.009431 0.43987 3.71517
14 4XMF HSM 0.03513 0.40094 3.80435
15 1I1Q TRP 0.02289 0.41278 4.16667
16 5U83 ZN8 0.02492 0.41498 4.24528
17 2PS1 ORO 0.03808 0.40118 4.42478
18 2XG5 EC2 0.008025 0.44879 4.62428
19 2XG5 EC5 0.008025 0.44879 4.62428
20 2VDF OCT 0.000171 0.51992 4.74308
21 4MMP SLB 0.01654 0.40858 5.19481
22 4H2W AMP 0.002801 0.44162 5.20231
23 4H2V AMP 0.006562 0.41056 5.20231
24 4H2W 5GP 0.0114 0.40941 5.20231
25 3MF2 AMP 0.008112 0.4036 5.20231
26 3ESS 18N 0.0303 0.41546 5.21739
27 5TFZ 7BC 0.01354 0.42466 5.33333
28 1LFO OLA 0.001007 0.45385 5.46875
29 5D9G GLU ASN LEU TYR PHE GLN 0.03462 0.40336 5.69106
30 1UGY GLA BGC 0.0166 0.42888 6.01504
31 4M26 AKG 0.02223 0.41974 6.04396
32 3HNT AXR BXY BXY BXX 0.01556 0.41352 6.07477
33 2J5B TYE 0.02307 0.42442 6.32184
34 2C49 ADN 0.01174 0.40882 6.95364
35 4XCP PLM 0.03579 0.40732 7.05882
36 1UH4 GLC GLC GLC GLC GLC GLC 0.03783 0.40831 8.01688
37 5HSS 64Z 0.03716 0.40174 8.08625
38 1NC2 DOE 0.03802 0.40141 8.83721
39 1WUW TSU 0.0333 0.41231 8.88889
40 3O5X JZG 0.02876 0.40024 9.05797
41 2WDQ CBE 0.008367 0.44228 9.30233
42 4IAW LIZ 0.02161 0.41014 9.57447
43 4ETZ C2E 0.01992 0.4166 10.101
44 1XPJ TLA 0.01306 0.4426 10.3175
45 4WGF HX2 0.01673 0.42608 11.7073
46 3DX5 DHB 0.03135 0.40188 12.2378
47 1PJ6 FOL 0.00006938 0.50123 27.0042
48 4PAB THG 0.003195 0.43892 30.5907
49 3TFJ THG 0.0002811 0.45802 30.8943
50 1WOR RED 0.0001005 0.46847 34.3407
Pocket No.: 2; Query (leader) PDB : 5X1M; Ligand: THG; Similar sites found: 46
This union binding pocket(no: 2) in the query (biounit: 5x1m.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5HTX ADP 0.02327 0.40967 1.82232
2 5IFK HPA 0.04956 0.40293 1.92308
3 5KJW 53C 0.02843 0.41302 2.10773
4 3IGO ANP 0.01137 0.40139 2.1097
5 4OSP 2V4 0.0479 0.40079 2.28137
6 3GXO MQA 0.03266 0.40584 2.43902
7 3VKC FPQ 0.008452 0.40703 2.44755
8 1TKK ALA GLU 0.02237 0.4001 2.45902
9 4CJN QNZ 0.001774 0.4808 2.53165
10 4WVW SLT 0.01729 0.41804 2.77778
11 5TG5 JW8 0.02742 0.41564 2.85714
12 3WGC PLG 0.01592 0.40716 2.93255
13 3HQP OXL 0.02608 0.40817 2.95359
14 4DOE CBK 0.03708 0.40401 3.16456
15 4LH7 NMN 0.01105 0.43724 3.71517
16 4QB6 GCU XYP 0.02682 0.40865 4.26829
17 4D52 GIV 0.02105 0.41502 4.44444
18 4D52 GXL 0.02085 0.41499 4.44444
19 2XG5 EC2 0.008663 0.44792 4.62428
20 2XG5 EC5 0.008663 0.44792 4.62428
21 2VDF OCT 0.0001141 0.51173 4.74308
22 4MMP SLB 0.01815 0.40782 5.19481
23 4H2W AMP 0.002835 0.44271 5.20231
24 4H2V AMP 0.00641 0.41229 5.20231
25 4H2W 5GP 0.01272 0.40842 5.20231
26 3MF2 AMP 0.008584 0.4038 5.20231
27 1LFO OLA 0.0008308 0.45907 5.46875
28 1E5Q SHR 0.01076 0.41888 5.55556
29 4DSU BZI 0.01304 0.43825 5.82011
30 1UGY GLA BGC 0.01311 0.43959 6.01504
31 4M26 AKG 0.02009 0.42323 6.04396
32 2D3Y DU 0.02195 0.40517 6.84932
33 1UH4 GLC GLC GLC GLC GLC GLC 0.03889 0.40895 8.01688
34 1WUW TSU 0.02979 0.4161 8.88889
35 3O5X JZG 0.02696 0.40281 9.05797
36 2WDQ CBE 0.009251 0.4407 9.30233
37 4YRD 3IT 0.02741 0.41289 9.47075
38 4ETZ C2E 0.01746 0.42165 10.101
39 1XPJ TLA 0.01127 0.45147 10.3175
40 4WGF HX2 0.02767 0.41344 11.7073
41 1XIM XYL 0.0281 0.40548 12.9771
42 1DZK PRZ 0.01732 0.4054 15.2866
43 1PJ6 FOL 0.00007442 0.50152 27.0042
44 4PAB THG 0.002685 0.44383 30.5907
45 3TFJ THG 0.0002733 0.46005 30.8943
46 1WOR RED 0.0001323 0.46533 34.3407
Pocket No.: 3; Query (leader) PDB : 5X1M; Ligand: THG; 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: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5X1M; Ligand: DHB; 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: 5x1m.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5x1m.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5X1M; Ligand: DHB; 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: 5x1m.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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