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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 293 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 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....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 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 28Z 0.452174 0.838235
16 29D 0.452174 0.838235
17 29C 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 DXY 0.401786 0.777778
24 DXZ 0.401786 0.777778
25 DDF 0.4 0.910448
26 21V 0.4 0.910448
Ligand no: 2; Ligand: DHB; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 DHB 1 1
2 IHB 0.514286 0.72
3 FHB 0.514286 0.72
4 4A3 0.514286 0.655172
5 CHB 0.514286 0.72
6 CUQ 0.45 0.826087
7 3HB 0.428571 0.761905
8 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 with APoc: 115
This union binding pocket(no: 1) in the query (biounit: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z3U CRR 1.64706
2 2VL1 GLY GLY 1.68776
3 5M0T AKG 1.70068
4 5HTX ADP 1.82232
5 5IFK HPA 1.92308
6 5KJW 53C 2.10773
7 3IHB GLU 2.19298
8 1SDW IYT 2.2293
9 5U97 PIT 2.32068
10 3GXO MQA 2.43902
11 1DTL BEP 2.48447
12 4CJN QNZ 2.53165
13 5FAW CHT 2.53165
14 4IP7 FLC 2.53165
15 5E58 CPZ 2.74262
16 4WVW SLT 2.77778
17 3WGC PLG 2.93255
18 1VBH PEP 2.95359
19 6GNF ADP 2.95359
20 3HQP OXL 2.95359
21 5JSP DQY 2.98507
22 4XBA 5GP 3
23 2QK4 ATP 3.09735
24 4KCT PYR 3.16456
25 5HV0 AKG 3.22581
26 6MDE MEV 3.30033
27 2CW6 3HG 3.3557
28 1O5Q PYR 3.37553
29 5A0U CHT 3.37553
30 5M90 JIF 3.44828
31 3WCS MAN NAG 3.54331
32 4LH7 NMN 3.71517
33 1H5R THM 3.75427
34 4XMF HSM 3.80435
35 5W75 SUC 3.82653
36 1VMK GUN 3.97112
37 4GC1 MAN MAN 3.98551
38 4U36 TNR 4.16667
39 1I1Q TRP 4.16667
40 5U83 ZN8 4.24528
41 1MFI FHC 4.38596
42 1SU2 ATP 4.40252
43 2PS1 ORO 4.42478
44 5UL4 SAM 4.43038
45 4D52 GIV 4.44444
46 1OFZ FUL 4.48718
47 5DQ8 FLF 4.58333
48 2XG5 EC2 4.62428
49 2XG5 EC5 4.62428
50 2VDF OCT 4.74308
51 1P72 THM 4.79042
52 3HCH RSM 4.79452
53 4FK7 P34 4.80349
54 1BGV GLU 4.89978
55 4MMP SLB 5.19481
56 4H2W AMP 5.20231
57 4H2V AMP 5.20231
58 4H2W 5GP 5.20231
59 3MF2 AMP 5.20231
60 3ESS 18N 5.21739
61 5TFZ 7BC 5.33333
62 1LFO OLA 5.46875
63 2VQ5 HBA 5.47264
64 5D9G GLU ASN LEU TYR PHE GLN 5.69106
65 5OCG 9R5 5.82011
66 1UGY GLA BGC 6.01504
67 4M26 AKG 6.04396
68 3HNT AXR BXY BXY BXX 6.07477
69 2J5B TYE 6.32184
70 6FA4 D1W 6.35838
71 3WG3 A2G GAL NAG FUC 6.74157
72 1USF NAP 6.74157
73 2QPU QPU 6.91358
74 2C49 ADN 6.95364
75 4XCP PLM 7.05882
76 5TV6 PML 7.08333
77 6GH9 MIX 7.12329
78 2WDB NAG MAN 7.29167
79 4OK9 HIS 7.38255
80 4XWM CBI 7.38397
81 1HBK MYR 7.86517
82 1UH4 GLC GLC GLC GLC GLC GLC 8.01688
83 5HSS 64Z 8.08625
84 2G7C GLA GAL NAG 8.23529
85 1C3X 8IG 8.27068
86 6F3M ADN 8.47826
87 1NC2 DOE 8.83721
88 1WUW TSU 8.88889
89 3O5X JZG 9.05797
90 4DE3 DN8 9.12547
91 4DDY DN6 9.12547
92 5GLT BGC GAL NAG GAL 9.15493
93 2WDQ CBE 9.30233
94 4IAW LIZ 9.57447
95 3N1S 5GP 10.084
96 4ETZ C2E 10.101
97 1XPJ TLA 10.3175
98 3T3Z 9PL 10.3376
99 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 10.5263
100 3H0L ADP 10.6383
101 5YBL AKG 10.828
102 4WGF HX2 11.7073
103 1KJ1 MAN 11.9266
104 3DX5 DHB 12.2378
105 3Q8U ADP 12.7389
106 2GNK ATP 13.3929
107 4J6W CDP 15.8537
108 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG 20.3125
109 1LVW TYD 20.678
110 5H9P TD2 20.8861
111 1PJ6 FOL 27.0042
112 4PAB THG 30.5907
113 3TFJ THG 30.8943
114 1WOR RED 34.3407
115 2OYH GLY HIS ARG PRO 46.9697
Pocket No.: 2; Query (leader) PDB : 5X1M; Ligand: THG; Similar sites found with APoc: 113
This union binding pocket(no: 2) in the query (biounit: 5x1m.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 2Z3U CRR 1.64706
3 2VL1 GLY GLY 1.68776
4 5HTX ADP 1.82232
5 5IFK HPA 1.92308
6 3GL0 HXX 2.00573
7 5KJW 53C 2.10773
8 3IGO ANP 2.1097
9 3IHB GLU 2.19298
10 1SDW IYT 2.2293
11 4OSP 2V4 2.28137
12 5U97 PIT 2.32068
13 5N6C TLA 2.33333
14 3GXO MQA 2.43902
15 3VKC FPQ 2.44755
16 1TKK ALA GLU 2.45902
17 1DTL BEP 2.48447
18 4CJN QNZ 2.53165
19 5FAW CHT 2.53165
20 4IP7 FLC 2.53165
21 4WVW SLT 2.77778
22 3HYW DCQ 2.7907
23 5TG5 JW8 2.85714
24 3WGC PLG 2.93255
25 6GNF ADP 2.95359
26 3HQP OXL 2.95359
27 1DE6 RNS 3.05164
28 1LRH NLA 3.06748
29 2QK4 ATP 3.09735
30 4DOE CBK 3.16456
31 5HV0 AKG 3.22581
32 2PW0 TRC 3.27456
33 4CSD MFU 3.30882
34 2CW6 3HG 3.3557
35 5A0U CHT 3.37553
36 3WCS MAN NAG 3.54331
37 4LH7 NMN 3.71517
38 1H5R THM 3.75427
39 1H5S TMP 3.75427
40 5W75 SUC 3.82653
41 1VMK GUN 3.97112
42 4U36 TNR 4.16667
43 4MOB ADP 4.21687
44 4QB6 GCU XYP 4.26829
45 1MFI FHC 4.38596
46 1SU2 ATP 4.40252
47 5UL4 SAM 4.43038
48 4D52 GXL 4.44444
49 4D52 GIV 4.44444
50 1OFZ FUL 4.48718
51 2XG5 EC5 4.62428
52 2XG5 EC2 4.62428
53 2VDF OCT 4.74308
54 3HCH RSM 4.79452
55 4FK7 P34 4.80349
56 1BGV GLU 4.89978
57 6F8B CXH 4.98339
58 4MMP SLB 5.19481
59 4H2W AMP 5.20231
60 4H2V AMP 5.20231
61 4H2W 5GP 5.20231
62 3MF2 AMP 5.20231
63 1LFO OLA 5.46875
64 1E5Q SHR 5.55556
65 4N7C AEF 5.68182
66 5OCG 9R5 5.82011
67 1UGY GLA BGC 6.01504
68 4M26 AKG 6.04396
69 6FA4 D1W 6.35838
70 1LSH PLD 6.54008
71 1USF NAP 6.74157
72 3WG3 A2G GAL NAG FUC 6.74157
73 3TA2 AKG 6.77966
74 2D3Y DU 6.84932
75 5TV6 PML 7.08333
76 5VNF VAL THR SER VAL VAL 7.59494
77 6CB2 OLC 7.84983
78 1UH4 GLC GLC GLC GLC GLC GLC 8.01688
79 4V1F BQ1 8.13953
80 2G7C GLA GAL NAG 8.23529
81 1C3X 8IG 8.27068
82 6F3M ADN 8.47826
83 1WUW TSU 8.88889
84 3O5X JZG 9.05797
85 4DDY DN6 9.12547
86 5GLT BGC GAL NAG GAL 9.15493
87 2WDQ CBE 9.30233
88 1WHT BZS 9.375
89 4YRD 3IT 9.47075
90 1C1L GAL BGC 9.48905
91 3N1S 5GP 10.084
92 4ETZ C2E 10.101
93 1XPJ TLA 10.3175
94 3T3Z 9PL 10.3376
95 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 10.5263
96 3H0L ADP 10.6383
97 5YBL AKG 10.828
98 4WGF HX2 11.7073
99 3Q8U ADP 12.7389
100 1XIM XYL 12.9771
101 6GW4 CHO 13.355
102 2GNK ATP 13.3929
103 6DZN AE3 14.0845
104 1DZK PRZ 15.2866
105 6FOF LAT 16.8367
106 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG 20.3125
107 1LVW TYD 20.678
108 5H9P TD2 20.8861
109 1PJ6 FOL 27.0042
110 4PAB THG 30.5907
111 3TFJ THG 30.8943
112 5Z84 CHD 32.6087
113 1WOR RED 34.3407
Pocket No.: 3; Query (leader) PDB : 5X1M; Ligand: THG; Similar sites found with APoc: 38
This union binding pocket(no: 3) in the query (biounit: 5x1m.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 5M0T AKG 1.70068
2 5E58 CPZ 2.74262
3 1VBH PEP 2.95359
4 5JSP DQY 2.98507
5 4XBA 5GP 3
6 4KCT PYR 3.16456
7 6MDE MEV 3.30033
8 1O5Q PYR 3.37553
9 5M90 JIF 3.44828
10 4XMF HSM 3.80435
11 4GC1 MAN MAN 3.98551
12 1I1Q TRP 4.16667
13 5U83 ZN8 4.24528
14 2PS1 ORO 4.42478
15 5DQ8 FLF 4.58333
16 1P72 THM 4.79042
17 3ESS 18N 5.21739
18 5TFZ 7BC 5.33333
19 2VQ5 HBA 5.47264
20 5D9G GLU ASN LEU TYR PHE GLN 5.69106
21 3HNT AXR BXY BXY BXX 6.07477
22 2J5B TYE 6.32184
23 2QPU QPU 6.91358
24 2C49 ADN 6.95364
25 4XCP PLM 7.05882
26 6GH9 MIX 7.12329
27 2WDB NAG MAN 7.29167
28 4OK9 HIS 7.38255
29 4XWM CBI 7.38397
30 1HBK MYR 7.86517
31 5HSS 64Z 8.08625
32 1NC2 DOE 8.83721
33 4DE3 DN8 9.12547
34 4IAW LIZ 9.57447
35 1KJ1 MAN 11.9266
36 3DX5 DHB 12.2378
37 4J6W CDP 15.8537
38 2OYH GLY HIS ARG PRO 46.9697
Pocket No.: 4; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: 33
This union binding pocket(no: 4) in the query (biounit: 5x1m.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5Y79 3PG 2.12766
2 2WL9 MBD 2.62295
3 3HYW DCQ 2.7907
4 5TG5 JW8 2.85714
5 6D61 4AA 3.07692
6 1RZM PEP 3.25444
7 4CSD MFU 3.30882
8 4LED XXR 3.35821
9 5YRI GLC GLC 3.52113
10 1H5S TMP 3.75427
11 4NZF ARB 3.79464
12 1W62 PYC 3.86473
13 5W3Y ACO 4.26136
14 4QB6 GCU XYP 4.26829
15 3BRN SRO 4.4586
16 3ZXE PGZ 4.51128
17 6F8B CXH 4.98339
18 4RF7 ARG 5.48523
19 1E5Q SHR 5.55556
20 4OIT MAN 6.19469
21 1LSH PLD 6.54008
22 3TA2 AKG 6.77966
23 2D3Y DU 6.84932
24 5VNF VAL THR SER VAL VAL 7.59494
25 3VV1 GAL FUC 8.125
26 4V1F BQ1 8.13953
27 1NC4 DOF 8.83721
28 1WHT BZS 9.375
29 4YRD 3IT 9.47075
30 3IWD M2T 10.2941
31 5AAV GW5 12.3016
32 5NFB 8VT 18.75
33 5Z84 CHD 32.6087
Pocket No.: 5; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: 25
This union binding pocket(no: 5) in the query (biounit: 5x1m.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 3GE7 AFQ 1.29534
3 5YSQ INS 1.74825
4 3GL0 HXX 2.00573
5 4UOZ GLA 2.1097
6 4G17 0VN 2.12121
7 4OSP 2V4 2.28137
8 5HC0 NPO 2.53165
9 1I06 TZL 2.77778
10 5I8T LAC 2.7933
11 1LRH NLA 3.06748
12 5YJS SAL 3.58974
13 4D52 GXL 4.44444
14 3MPB FRU 4.87805
15 4WCX MET 5.6962
16 1DCP HBI 5.76923
17 6DIO CIT 6.75991
18 6CB2 OLC 7.84983
19 3LPP KTL 8.01688
20 6F5W KG1 8.94309
21 4C1K PEP 9.54198
22 1WKM MET 11.5254
23 1XIM XYL 12.9771
24 2IDO TMP 15.6627
25 6FOF LAT 16.8367
Pocket No.: 6; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: 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 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: 12
This union binding pocket(no: 7) in the query (biounit: 5x1m.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
1 3OND NAD 2.1097
2 3OND ADN 2.1097
3 1V8B NAD 2.74262
4 3DSK T25 3.43434
5 5AE2 FAD 4.10334
6 5AE2 FYC 4.10334
7 4L2I FAD 4.33526
8 5BSZ THM 4.8
9 2F57 23D 6.30915
10 6F3M NAD 8.47826
11 1L7E NAI 9.89583
12 1ZUI SKM 10.7143
Pocket No.: 8; Query (leader) PDB : 5X1M; Ligand: DHB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5x1m.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
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