Receptor
PDB id Resolution Class Description Source Keywords
3KL3 2.33 Å EC: 3.2.1.136 CRYSTAL STRUCTURE OF LIGAND BOUND XYNC BACILLUS SUBTILIS ALPHA-BETA BARREL (BETA/ALPHA)8 BARREL (BETA/ALPHA)8 + BETGLUCURONATE COORDINATION BY XYNC GLYCOSIDASE HYDROLASE POLYSACCHARIDE DEGRADATION GLYCOSYL HYDROLASE
Ref.: LIGAND BOUND STRUCTURES OF A GLYCOSYL HYDROLASE FAM GLUCURONOXYLAN XYLANOHYDROLASE. J.MOL.BIOL. V. 407 92 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BDP B:402;
Valid;
none;
submit data
194.139 C6 H10 O7 [C@@H...
DHI A:403;
B:404;
Valid;
Valid;
none;
none;
submit data
156.162 C6 H10 N3 O2 c1c([...
GCU A:402;
B:403;
Valid;
Valid;
none;
none;
submit data
194.139 C6 H10 O7 [C@@H...
PG4 B:405;
C:402;
Invalid;
Invalid;
none;
none;
submit data
194.226 C8 H18 O5 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KL3 2.33 Å EC: 3.2.1.136 CRYSTAL STRUCTURE OF LIGAND BOUND XYNC BACILLUS SUBTILIS ALPHA-BETA BARREL (BETA/ALPHA)8 BARREL (BETA/ALPHA)8 + BETGLUCURONATE COORDINATION BY XYNC GLYCOSIDASE HYDROLASE POLYSACCHARIDE DEGRADATION GLYCOSYL HYDROLASE
Ref.: LIGAND BOUND STRUCTURES OF A GLYCOSYL HYDROLASE FAM GLUCURONOXYLAN XYLANOHYDROLASE. J.MOL.BIOL. V. 407 92 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3KL3 - DHI C6 H10 N3 O2 c1c([nH+]c....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 5A6L - XYP XYP n/a n/a
2 4UQA - HIS C6 H10 N3 O2 c1c([nH+]c....
3 5A6M - XYP XYP n/a n/a
4 4UQC - GLC C6 H12 O6 C([C@@H]1[....
5 4CKQ - MLA C3 H4 O4 C(C(=O)O)C....
6 3KL3 - DHI C6 H10 N3 O2 c1c([nH+]c....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 5A6L - XYP XYP n/a n/a
2 4UQA - HIS C6 H10 N3 O2 c1c([nH+]c....
3 5A6M - XYP XYP n/a n/a
4 4UQC - GLC C6 H12 O6 C([C@@H]1[....
5 4CKQ - MLA C3 H4 O4 C(C(=O)O)C....
6 3KL3 - DHI C6 H10 N3 O2 c1c([nH+]c....
7 2Y24 - XYP XYP GCV XYP n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BDP; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 ADA 1 1
2 BDP 1 1
3 GTR 1 1
4 GCU 1 1
5 AD0 0.458333 0.821429
6 GCW 0.45 0.884615
7 GCV 0.45 0.884615
8 TGU 0.423077 0.821429
Ligand no: 2; Ligand: DHI; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 HIS 1 1
2 DHI 1 1
3 HSO 0.52381 0.846154
Ligand no: 3; Ligand: GCU; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 ADA 1 1
2 BDP 1 1
3 GTR 1 1
4 GCU 1 1
5 AD0 0.458333 0.821429
6 GCW 0.45 0.884615
7 GCV 0.45 0.884615
8 TGU 0.423077 0.821429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KL3; Ligand: DHI; Similar sites found: 4
This union binding pocket(no: 1) in the query (biounit: 3kl3.bio2) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IYF UDP 0.02305 0.40055 2.24439
2 4A0S CO8 0.0252 0.44204 2.99252
3 3KIH GDL 0.00611 0.42521 9.27835
4 4II2 ATP 0.01308 0.43574 11.6564
Pocket No.: 2; Query (leader) PDB : 3KL3; Ligand: BDP; 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: 3kl3.bio2) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3KL3; Ligand: GCU; Similar sites found: 16
This union binding pocket(no: 3) in the query (biounit: 3kl3.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ICC NAP 0.03823 0.40192 1.96078
2 1HXD BTN 0.02297 0.40449 2.18069
3 4I06 X8A 0.04203 0.40399 2.94118
4 5G5G FAD 0.02151 0.43254 3.45912
5 2FT0 ACO 0.01074 0.41619 3.82979
6 2Y4N PAC 0.03791 0.40333 3.99003
7 3ZOK NAD 0.0259 0.41131 4.7619
8 3A4T SFG 0.01215 0.40419 5.10949
9 4C3Y FAD 0.01853 0.42621 5.73566
10 2HV8 GTP 0.03651 0.40027 5.81395
11 2D7C GTP 0.02653 0.42009 5.98802
12 3MMR ABH 0.03423 0.41132 6.98254
13 1T3Q FAD 0.03275 0.40407 7.7381
14 3RGG AIR 0.009567 0.40725 8.80503
15 1XSE NDP 0.01905 0.43011 10.1695
16 1FIQ FAD 0.008928 0.44148 11.9701
Pocket No.: 4; Query (leader) PDB : 3KL3; Ligand: GCU; Similar sites found: 30
This union binding pocket(no: 4) in the query (biounit: 3kl3.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L8F MTX 0.00868 0.4021 1.60256
2 4CNE SAH 0.009728 0.40022 1.87266
3 2CHG ANP 0.02603 0.40433 2.21239
4 5H04 NAI 0.01868 0.41926 2.24439
5 2EJU SAH 0.008152 0.407 2.38095
6 4H8N NDP 0.006205 0.4017 2.58065
7 3GPO APR 0.005105 0.45378 2.97619
8 4ZH7 FUC GAL NAG GAL FUC 0.0358 0.40325 2.99252
9 1OG1 TAD 0.02371 0.40012 3.09735
10 2E5A LAQ 0.02393 0.42924 3.45821
11 2RNF UM3 0.003868 0.41065 4.16667
12 1XK9 P34 0.006465 0.4266 4.18605
13 2V0C ANZ 0.003005 0.45566 4.2394
14 5FA6 NAP 0.01494 0.41497 4.2394
15 5FA6 FMN 0.01469 0.41497 4.2394
16 5FA6 FAD 0.01469 0.41497 4.2394
17 3B82 NAD 0.004518 0.48294 4.34783
18 4R81 FMN 0.02572 0.42887 4.36893
19 4K30 NLG 0.01866 0.40156 4.375
20 3ESS 18N 0.002755 0.43633 5.65217
21 2WZM NA7 0.01593 0.40438 5.65371
22 4K47 WMP 0.002775 0.44547 6.25
23 5ARK UMP 0.004592 0.40643 6.71642
24 2A9K NAD 0.02446 0.40501 8.52018
25 2GQT FAD 0.04009 0.40317 8.95522
26 1GZF NIR 0.01172 0.41573 9.00474
27 1GZF ADP 0.01881 0.41573 9.00474
28 1GZF NAD 0.02628 0.40006 9.00474
29 4JIZ TYR HIS SEP VAL VAL ARG TYR ALA 0.01139 0.42435 11.6279
30 4Y24 TD2 0.01114 0.43297 11.6883
Pocket No.: 5; Query (leader) PDB : 3KL3; Ligand: DHI; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 3kl3.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WQT ANP 0.007049 0.40717 2.47934
2 1YB5 NAP 0.009063 0.40738 3.9886
3 3KIF GDL 0.0009862 0.43373 4.71698
4 3EPO MP5 0.01585 0.41342 7.4813
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