Receptor
PDB id Resolution Class Description Source Keywords
1V6V 2.1 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 COMPLEXED WITH 3(2)-ALPHA-L- A RABINOFURANOSYL-XYLOTRIOSE STREPTOMYCES OLIVACEOVIRIDIS ALPHA-BETA BARREL PROTEIN-SUGAR COMPLEX CARBOHYDRATE BINDING MODULE HYDROLASE
Ref.: CRYSTAL STRUCTURES OF DECORATED XYLOOLIGOSACCHARIDES BOUND TO A FAMILY 10 XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 J.BIOL.CHEM. V. 279 9606 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XYP B:961;
Valid;
none;
submit data
150.13 C5 H10 O5 C1[C@...
XYP AHR XYP XYP A:450;
A:471;
B:950;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
546.475 n/a O(C1C...
XYP XYP A:456;
B:956;
B:970;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
164.157 n/a O(C)C...
XYP XYP XYP A:461;
Valid;
none;
submit data
414.36 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D24 1.85 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF ES COMPLEX OF CATALYTIC-SITE MUTANT XYL STREPTOMYCES OLIVACEOVIRIDIS E-86 STREPTOMYCES OLIVACEOVIRIDIS TIM-BARREL RETAINING ENZYME CATALYTIC-SITE MUTANT CHEMICAMICHAELIS COMPLEX HYDROLASE
Ref.: CRYSTALLOGRAPHIC SNAPSHOTS OF AN ENTIRE REACTION CY RETAINING XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDI J.BIOCHEM. V. 146 61 2009
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP C5 H10 O5 C1[C@H]([C....
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP C5 H10 O5 C1[C@H]([C....
6 1V6X - XYP C5 H10 O5 C1[C@H]([C....
7 1V6V - XYP AHR XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS XYS AZI n/a n/a
10 1IT0 - LAT C12 H22 O11 C([C@@H]1[....
11 1ISW - XYP XYP n/a n/a
12 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
13 1ISV - XYP C5 H10 O5 C1[C@H]([C....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP C5 H10 O5 C1[C@H]([C....
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP C5 H10 O5 C1[C@H]([C....
6 1V6X - XYP C5 H10 O5 C1[C@H]([C....
7 1V6V - XYP AHR XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS XYS AZI n/a n/a
10 1IT0 - LAT C12 H22 O11 C([C@@H]1[....
11 1ISW - XYP XYP n/a n/a
12 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
13 1ISV - XYP C5 H10 O5 C1[C@H]([C....
50% Homology Family (53)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1V0M - XDN XYP n/a n/a
2 1V0N - XIF XYP n/a n/a
3 1V0K Ki = 50 uM XYP XDN n/a n/a
4 1V0L Ki = 480 nM XIF XYP n/a n/a
5 1OD8 - XDL XYP n/a n/a
6 3W25 - XYP XYP n/a n/a
7 3W27 - XYP XYS n/a n/a
8 3W26 - XYP XYP XYP n/a n/a
9 3W29 - XYP XYP XYP XYS n/a n/a
10 3W28 - XYP XYP XYS n/a n/a
11 1B30 - XYP XYP XYP n/a n/a
12 1B3V - XYS C5 H10 O5 C1[C@H]([C....
13 1B3Y - XYS C5 H10 O5 C1[C@H]([C....
14 1B3X - XYP XYP XYP n/a n/a
15 1B3Z - XYP XYP XYP n/a n/a
16 1ISY - BGC C6 H12 O6 C([C@@H]1[....
17 1V6W - XYP C5 H10 O5 C1[C@H]([C....
18 1ISX - XYP XYP n/a n/a
19 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
20 1V6U - XYP C5 H10 O5 C1[C@H]([C....
21 1V6X - XYP C5 H10 O5 C1[C@H]([C....
22 1V6V - XYP AHR XYP XYP n/a n/a
23 2D24 - XYS XYS n/a n/a
24 2D23 - XYS XYS AZI n/a n/a
25 1IT0 - LAT C12 H22 O11 C([C@@H]1[....
26 1ISW - XYP XYP n/a n/a
27 2D20 - NPO C6 H5 N O3 c1cc(ccc1[....
28 1ISV - XYP C5 H10 O5 C1[C@H]([C....
29 4BS0 Ki = 2 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
30 3EMZ - HXH C19 H21 N O4 c1ccc(cc1)....
31 3WUE - XYP C5 H10 O5 C1[C@H]([C....
32 3WUG - XYP C5 H10 O5 C1[C@H]([C....
33 1FH7 Ki = 5.8 uM XYP XDN n/a n/a
34 1FHD Ki = 0.15 uM XYP XIM n/a n/a
35 1FH8 Ki = 0.13 uM XYP XIF n/a n/a
36 1J01 Ki = 0.34 uM XIL C10 H17 N O7 C1CNC(=O)[....
37 1FH9 Ki = 0.37 uM XYP LOX n/a n/a
38 5D4Y - BXP C10 H18 O9 C1[C@H]([C....
39 2FGL - XYS XYS n/a n/a
40 3NJ3 - XYP XYP n/a n/a
41 1VBR - XYS XYP n/a n/a
42 2BNJ - XYP XYP AHR FER n/a n/a
43 1GOR - XYP XYS n/a n/a
44 3NYD - 3NY C6 H4 N4 O2 c1cc2c(cc1....
45 1GOQ - XYP XYP n/a n/a
46 1UQY - XYP XYP XYP XYP n/a n/a
47 1UR1 - XYS XYP AHR n/a n/a
48 1UQZ - XYP XYP XYP GCV n/a n/a
49 3RDK - GCV XYP XYP XYS n/a n/a
50 5OFK - XYP XYP XYP XYP XYP XYP XYP n/a n/a
51 5OFL Ka = 17500 M^-1 BGC BGC BGC BGC BGC BGC n/a n/a
52 1R87 - XYP XYP n/a n/a
53 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XYP; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 RIP 1 1
2 XYS 1 1
3 ARB 1 1
4 HSY 1 1
5 ARA 1 1
6 XYP 1 1
7 LXC 1 1
8 0MK 1 1
9 XYP XYS 0.414634 0.84375
10 BXP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 FU4 0.4 0.896552
Ligand no: 2; Ligand: XYP AHR XYP XYP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP AHR XYP XYP 1 1
2 XYP XYP XYP AHR 1 1
3 XYS XYP AHR XYP 1 1
4 AHR XYS XYP XYP XYP 0.771429 1
5 AHR XYP XYP 0.7 1
6 XYS XYP AHR 0.7 1
7 XYP XYP AHR 0.7 1
8 AHR XYP XYP XYP 0.689189 1
9 AHR XYS XYS 0.676056 1
10 BXP 0.603175 0.888889
11 XYS XYP 0.603175 0.888889
12 XYP XYS 0.603175 0.888889
13 XYP XYP XYP XYP XYP XYP 0.590909 0.888889
14 XYS XYS XYS XYS XYS 0.590909 0.888889
15 XYP XYP XYS 0.590909 0.888889
16 XYP XYP XYP XYP 0.590909 0.888889
17 XYS XYS XYS XYS 0.590909 0.888889
18 XYP XYP XYP XYP XYP XYP XYP 0.590909 0.888889
19 XYP XYP XYP XYP XYP 0.590909 0.888889
20 XYP XYP XYP XYS 0.590909 0.888889
21 XYP XYS XYP 0.590909 0.888889
22 XYP XYP XYP 0.590909 0.888889
23 XYS XYP XYP 0.590909 0.888889
24 GLC GLC XYP 0.552632 0.916667
25 XYP XYP XYP FX3 0.542056 0.795455
26 XYS XYS XYS 0.486111 0.864865
27 XYP XYP GCV XYP 0.473118 0.8
28 KHO 0.444444 0.972222
29 GCV XYP XYP XYP 0.431579 0.8
30 XYP XYP XYP GCV 0.431579 0.8
31 GCV XYP XYP XYS 0.431579 0.8
32 XLM 0.428571 0.894737
33 GCV XYP XYP 0.413043 0.8
34 XYP XYP AHR FER 0.40708 0.795455
Ligand no: 3; Ligand: XYP XYP; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 ARW 1 1
2 XYP XYP 1 1
3 X1P 0.461538 0.651163
4 XS2 0.44 0.842105
5 XLM 0.431373 0.837838
6 XYP XYS 0.422222 0.828571
7 XYS XYP 0.422222 0.828571
8 BXP 0.422222 0.828571
Ligand no: 4; Ligand: XYP XYP XYP; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYS XYS XYS XYS 1 1
2 XYP XYP XYP XYP 1 1
3 XYP XYP XYS 1 1
4 XYS XYS XYS XYS XYS 1 1
5 XYP XYP XYP XYP XYP XYP 1 1
6 XYP XYP XYP XYP XYP XYP XYP 1 1
7 XYS XYP XYP 1 1
8 XYP XYP XYP 1 1
9 XYP XYP XYP XYS 1 1
10 XYP XYS XYP 1 1
11 XYP XYP XYP XYP XYP 1 1
12 BXP 0.904762 1
13 XYS XYP 0.904762 1
14 XYP XYS 0.904762 1
15 XYS XYS XYS 0.791667 0.969697
16 XYP XYP XYP AHR 0.590909 0.888889
17 XYS XYP AHR XYP 0.590909 0.888889
18 XYP AHR XYP XYP 0.590909 0.888889
19 AHR XYP XYP XYP 0.575758 0.888889
20 AHR XYS XYP XYP XYP 0.560606 0.888889
21 XYS XYS 0.511111 0.939394
22 XYP XYP TRS 0.508197 0.711111
23 XYP XYP GCV XYP 0.506494 0.888889
24 XYS XYS AZI 0.5 0.653061
25 XYP XYP XYP GCV 0.493506 0.888889
26 GCV XYP XYP XYS 0.493506 0.888889
27 GCV XYP XYP XYP 0.493506 0.888889
28 AHR XYP XYP 0.484848 0.888889
29 XYP XYP AHR 0.484848 0.888889
30 XYS XYP AHR 0.484848 0.888889
31 AHR XYS XYS 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XYP XDN 0.438596 0.704545
34 XIF XYP 0.438596 0.659574
35 XYP XIF 0.438596 0.659574
36 XDN XYP 0.438596 0.704545
37 GCV XYP XYP 0.415584 0.888889
38 GLC GLC XYP 0.405797 0.911765
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D24; Ligand: XYS XYS XYS XYS XYS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2d24.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2D24; Ligand: XYS XYS; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 2d24.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3AJ6 NGA 6.29371
2 2ZQO NGA 6.92308
3 5MUA GAL 16.4336
4 4OUJ LBT 16.9381
5 4ZGR NGA GAL 18.7739
6 4LO2 GAL BGC 19.7279
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