Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:980;
B:981;
B:982;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:970;
A:971;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
XYS XYS G:1;
E:1;
Valid;
Valid;
none;
none;
submit data
282.245 n/a O(C1C...
XYS XYS XYS XYS D:1;
Valid;
none;
submit data
546.475 n/a O(C1C...
XYS XYS XYS XYS XYS F:1;
C:1;
Valid;
Valid;
none;
none;
submit data
678.59 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 32 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP XYP n/a n/a
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP XYP n/a n/a
6 1V6X - XYP XYP n/a n/a
7 1V6V - XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS AZI XYS n/a n/a
10 1IT0 - BGC GAL n/a n/a
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 30 families.
1 1ISY - BGC C6 H12 O6 C([C@@H]1[....
2 1V6W - XYP XYP n/a n/a
3 1ISX - XYP XYP n/a n/a
4 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
5 1V6U - XYP XYP n/a n/a
6 1V6X - XYP XYP n/a n/a
7 1V6V - XYP XYP n/a n/a
8 2D24 - XYS XYS n/a n/a
9 2D23 - XYS AZI XYS n/a n/a
10 1IT0 - BGC GAL n/a n/a
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 18 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 - XYS XYP n/a n/a
8 3W26 - XYP XYP XYP n/a n/a
9 3W29 - XYS XYP XYP XYP n/a n/a
10 3W28 - XYS XYP XYP 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 XYP n/a n/a
18 1ISX - XYP XYP n/a n/a
19 1ISZ - GAL C6 H12 O6 C([C@@H]1[....
20 1V6U - XYP XYP n/a n/a
21 1V6X - XYP XYP n/a n/a
22 1V6V - XYP XYP n/a n/a
23 2D24 - XYS XYS n/a n/a
24 2D23 - XYS AZI XYS n/a n/a
25 1IT0 - BGC GAL n/a n/a
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 LOX XYP n/a n/a
38 5D4Y - XYP XYP n/a n/a
39 2FGL - XYS XYS n/a n/a
40 3NJ3 - XYP XYP n/a n/a
41 1VBR - XYP XYS n/a n/a
42 2BNJ - XYP XYP AHR FER n/a n/a
43 1GOR - XYS XYP 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 - XYS XYP XYP GCV 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: XYS XYS; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 XYS XYS 1 1
2 XYS XYS XYS 0.590909 0.969697
3 XYS XYP 0.560976 0.939394
4 BXP 0.560976 0.939394
5 XYP XYS 0.560976 0.939394
6 XYP XYP XYP XYP 0.511111 0.939394
7 XYP XYP XYS 0.511111 0.939394
8 XYP XYP XYP XYP XYP 0.511111 0.939394
9 XYS XYP XYP 0.511111 0.939394
10 XYS XYS XYS XYS 0.511111 0.939394
11 XYP XYP XYP 0.511111 0.939394
12 XYP XYP XYP XYS 0.511111 0.939394
13 XYP XYP XYP XYP XYP XYP XYP 0.511111 0.939394
14 XYS XYS XYS XYS XYS 0.511111 0.939394
15 XYP XYS XYP 0.511111 0.939394
16 XYP XYP XYP XYP XYP XYP 0.511111 0.939394
Ligand no: 2; Ligand: XYS XYS XYS XYS; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP XYP XYP XYP 1 1
2 XYS XYP XYP 1 1
3 XYP XYP XYP XYP XYP XYP 1 1
4 XYP XYP XYS 1 1
5 XYP XYS XYP 1 1
6 XYS XYS XYS XYS XYS 1 1
7 XYS XYS XYS XYS 1 1
8 XYP XYP XYP XYS 1 1
9 XYP XYP XYP XYP XYP XYP XYP 1 1
10 XYP XYP XYP XYP XYP 1 1
11 XYP XYP XYP 1 1
12 XYP XYS 0.904762 1
13 BXP 0.904762 1
14 XYS XYP 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 XYP 0.493506 0.888889
27 GCV XYP XYP XYS 0.493506 0.888889
28 XYS XYP AHR 0.484848 0.888889
29 AHR XYP XYP 0.484848 0.888889
30 AHR XYS XYS 0.484848 0.888889
31 XYP XYP AHR 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XDN XYP 0.438596 0.704545
34 XYP XIF 0.438596 0.659574
35 XYP XDN 0.438596 0.704545
36 XIF XYP 0.438596 0.659574
37 GCV XYP XYP 0.415584 0.888889
38 GLC GLC XYP 0.405797 0.911765
Ligand no: 3; Ligand: XYS XYS XYS XYS XYS; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP XYP XYP XYP 1 1
2 XYS XYP XYP 1 1
3 XYP XYP XYP XYP XYP XYP 1 1
4 XYP XYP XYS 1 1
5 XYP XYS XYP 1 1
6 XYS XYS XYS XYS XYS 1 1
7 XYS XYS XYS XYS 1 1
8 XYP XYP XYP XYS 1 1
9 XYP XYP XYP XYP XYP XYP XYP 1 1
10 XYP XYP XYP XYP XYP 1 1
11 XYP XYP XYP 1 1
12 XYP XYS 0.904762 1
13 BXP 0.904762 1
14 XYS XYP 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 XYP 0.493506 0.888889
27 GCV XYP XYP XYS 0.493506 0.888889
28 XYS XYP AHR 0.484848 0.888889
29 AHR XYP XYP 0.484848 0.888889
30 AHR XYS XYS 0.484848 0.888889
31 XYP XYP AHR 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XDN XYP 0.438596 0.704545
34 XYP XIF 0.438596 0.659574
35 XYP XDN 0.438596 0.704545
36 XIF XYP 0.438596 0.659574
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: 15
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 3AJ6 NGA 6.29371
3 2ZQO NGA 6.92308
4 2ZQO NGA 6.92308
5 2ZQO NGA 6.92308
6 2ZQO NGA 6.92308
7 5MUA GAL 16.4336
8 5MUA GAL 16.4336
9 4OUJ LBT 16.9381
10 4OUJ LBT 16.9381
11 4OUJ LBT 16.9381
12 4OUJ LBT 16.9381
13 4ZGR NGA GAL 18.7739
14 4LO2 GAL BGC 19.7279
15 4LO2 GAL BGC 19.7279
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