Receptor
PDB id Resolution Class Description Source Keywords
1R87 1.67 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF THE EXTRACELLULAR XYLANASE FROM GEOBACI STEAROTHERMOPHILUS T-6 (XT6, MONOCLINIC FORM): THE COMPLEX E NZYME WITH XYLOPENTAOSE AT 1.67A RESOLUTION GEOBACILLUS STEAROTHERMOPHILUS HYDROLASE
Ref.: MAPPING GLYCOSIDE HYDROLASE SUBSTRATE SUBSITES BY I TITRATION CALORIMETRY. PROC.NATL.ACAD.SCI.USA V. 101 11275 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:701;
A:702;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
SO4 A:801;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
XYP XYP A:448;
Valid;
none;
submit data
282.245 n/a O(C1O...
XYP XYP XYP A:450;
Valid;
none;
submit data
414.36 n/a O(C1O...
ZN A:901;
A:902;
A:903;
A:904;
A:905;
A:906;
A:907;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1R87 1.67 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF THE EXTRACELLULAR XYLANASE FROM GEOBACI STEAROTHERMOPHILUS T-6 (XT6, MONOCLINIC FORM): THE COMPLEX E NZYME WITH XYLOPENTAOSE AT 1.67A RESOLUTION GEOBACILLUS STEAROTHERMOPHILUS HYDROLASE
Ref.: MAPPING GLYCOSIDE HYDROLASE SUBSTRATE SUBSITES BY I TITRATION CALORIMETRY. PROC.NATL.ACAD.SCI.USA V. 101 11275 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1R87 - XYP XYP n/a n/a
2 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 2FGL - XYS XYS n/a n/a
2 1R87 - XYP XYP n/a n/a
3 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
50% Homology Family (52)
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 1UR2 - XYP XYP XYP n/a n/a
47 2CNC - XYS XYP AHR n/a n/a
48 1UR1 - XYS XYP AHR n/a n/a
49 1UQZ - XYP XYP XYP GCV n/a n/a
50 3RDK - GCV XYP XYP XYS n/a n/a
51 1R87 - XYP XYP n/a n/a
52 1HIZ - GLC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XYP XYP; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP XYP 1 1
2 XYS XYS 1 1
3 XYS XYP 1 1
4 BXP 1 1
5 XYP XYS 1 1
6 XYP XYP XYP XYP XYP XYP 0.904762 1
7 XYS XYP XYP 0.904762 1
8 XYP XYP XYP XYS 0.904762 1
9 XYS XYS XYS XYS 0.904762 1
10 XYS XYS XYS XYS XYS 0.904762 1
11 XYP XYP XYP XYP 0.904762 1
12 XYP XYS XYP 0.904762 1
13 XYP XYP XYS 0.904762 1
14 XYP XYP XYP 0.904762 1
15 XYP XYP XYP XYP XYP 0.904762 1
16 XYS XYS XYS 0.708333 0.969697
17 XYS XYP AHR XYP 0.603175 0.888889
18 XYP XYP XYP AHR 0.603175 0.888889
19 XYP AHR XYP XYP 0.603175 0.888889
20 XYS XYS AZI 0.537037 0.653061
21 XYP XYP AHR 0.516129 0.888889
22 AHR XYP XYP 0.516129 0.888889
23 XYS XYP AHR 0.516129 0.888889
24 AHR XYS XYS 0.516129 0.888889
25 AHR XYP XYP XYP 0.515152 0.888889
26 XYP XYP GCV XYP 0.513514 0.888889
27 AHR XYS XYP XYP XYP 0.5 0.888889
28 XYP XYP TRS 0.483333 0.744186
29 XYP XDN 0.471698 0.756098
30 XDN XYP 0.471698 0.756098
31 XIF XYP 0.462963 0.704545
32 XYP XIF 0.462963 0.704545
33 GCV XYP XYP XYS 0.441558 0.888889
34 GCV XYP XYP XYP 0.441558 0.888889
35 XYP XYP XYP GCV 0.441558 0.888889
36 XYS XYS NPO 0.439394 0.615385
37 GCV XYP XYP 0.438356 0.888889
38 ARW 0.422222 0.828571
39 XIL 0.416667 0.680851
40 XYP LOX 0.416667 0.603774
41 XDL XYP 0.416667 0.680851
42 XYP 0.414634 0.84375
43 HSY 0.414634 0.84375
44 ARB 0.414634 0.84375
45 ARA 0.414634 0.84375
46 0MK 0.414634 0.84375
47 LXC 0.414634 0.84375
48 XYS 0.414634 0.84375
49 RIP 0.414634 0.84375
50 GLC GLC XYP 0.409091 0.911765
Ligand no: 2; Ligand: XYP XYP XYP; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP XYP XYS 1 1
2 XYS XYS XYS XYS 1 1
3 XYS XYP XYP 1 1
4 XYP XYP XYP XYS 1 1
5 XYP XYP XYP XYP XYP 1 1
6 XYP XYP XYP XYP 1 1
7 XYP XYP XYP 1 1
8 XYP XYP XYP XYP XYP XYP 1 1
9 XYS XYS XYS XYS XYS 1 1
10 XYP XYS XYP 1 1
11 XYS XYS 0.904762 1
12 XYS XYP 0.904762 1
13 XYP XYS 0.904762 1
14 BXP 0.904762 1
15 XYP XYP 0.904762 1
16 XYS XYS XYS 0.791667 0.969697
17 XYS XYP AHR XYP 0.590909 0.888889
18 XYP XYP XYP AHR 0.590909 0.888889
19 XYP AHR XYP XYP 0.590909 0.888889
20 AHR XYP XYP XYP 0.575758 0.888889
21 AHR XYS XYP XYP XYP 0.560606 0.888889
22 XYP XYP GCV XYP 0.506494 0.888889
23 XYS XYS AZI 0.5 0.653061
24 XYP XYP TRS 0.5 0.744186
25 GCV XYP XYP XYS 0.493506 0.888889
26 XYP XYP XYP GCV 0.493506 0.888889
27 GCV XYP XYP XYP 0.493506 0.888889
28 AHR XYP XYP 0.484848 0.888889
29 AHR XYS XYS 0.484848 0.888889
30 XYP XYP AHR 0.484848 0.888889
31 XYS XYP AHR 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XDN XYP 0.438596 0.756098
34 XYP XDN 0.438596 0.756098
35 XYP XIF 0.431034 0.704545
36 XIF XYP 0.431034 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 : 1R87; Ligand: XYP XYP XYP; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 1r87.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4Y24 TD2 0.008841 0.41253 None
2 4U5I BXP 0.004662 0.43146 1.84697
3 1UAS GLA 0.007684 0.41997 2.48619
4 2NSX IFM 0.007954 0.41052 2.63852
5 5A7V MAN 0.008565 0.42372 2.90237
6 5AYI BGC 0.02179 0.40178 3.16623
7 5FYR INS 0.02063 0.40411 3.3557
8 5T9C G3P 0.0009724 0.47579 3.73134
9 4J6O CIT 0.01731 0.40802 3.78788
10 3A23 GAL 0.008296 0.4231 3.95778
11 1DE6 RNS 0.005846 0.41679 4.92958
12 4CD6 IFM BMA 0.008526 0.4225 5
13 4Y2B EPK 0.00468 0.43569 5.5409
14 1UZ4 IFL 0.0194 0.4067 5.5409
15 5M12 7D0 0.00394 0.42482 6.33245
16 5H9O GLC 0.01089 0.4185 7.95455
17 2QL9 CIT 0.01601 0.40361 9.27835
18 3T7V MD0 0.01947 0.40428 10.2857
19 5GNX BGC 0.01278 0.4153 10.8179
20 4D1J DGJ 0.008377 0.41712 12.4011
21 4PMZ BXP 0.00000000007821 0.83922 42.5743
Pocket No.: 2; Query (leader) PDB : 1R87; Ligand: XYP XYP; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 1r87.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CNK FAD 0.04591 0.40878 5.27704
2 4PMZ BXP 0.000004263 0.57505 42.5743
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