Receptor
PDB id Resolution Class Description Source Keywords
3NJ3 1.88 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF XYLANASE 10B FROM THERMOTOGA PETROPHILA COMPLEX WITH XYLOBIOSE THERMOTOGA PETROPHILA RKU-1 TIM BARREL XYLANASE HYDROLASE
Ref.: THERMAL-INDUCED CONFORMATIONAL CHANGES IN THE PRODU RELEASE AREA DRIVE THE ENZYMATIC ACTIVITY OF XYLANA CRYSTAL STRUCTURE, CONFORMATIONAL STABILITY AND FUN CHARACTERIZATION OF THE XYLANASE 10B FROM THERMOTOG PETROPHILA RKU-1. BIOCHEM.BIOPHYS.RES.COMM
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:342;
B:342;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SO4 A:343;
A:344;
B:343;
B:344;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
XYP XYP A:345;
B:345;
Valid;
Valid;
none;
none;
submit data
282.245 n/a O(C1O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VBR 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF COMPLEX XYLANASE 10B FROM THERMOTOGA MARITIMA WITH XYLOBIOSE THERMOTOGA MARITIMA XYLANASE 10B HYDROLASE
Ref.: STRUCTURAL BASIS OF THE SUBSTRATE SUBSITE AND THE HIGHLY THERMAL STABILITY OF XYLANASE 10B FROM THERMOTOGA MARITIMA MSB8 PROTEINS V. 61 999 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 3NJ3 - XYP XYP n/a n/a
2 1VBR - XYS XYP n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 3NJ3 - XYP XYP n/a n/a
2 1VBR - XYS XYP n/a n/a
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VBR; Ligand: XYS XYP; Similar sites found: 29
This union binding pocket(no: 1) in the query (biounit: 1vbr.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M67 NAD 0.04329 0.4145 1.21951
2 4Y2B EPK 0.002189 0.428 1.82927
3 4U5I BXP 0.004748 0.42076 1.82927
4 4FFG 0U8 0.01036 0.40696 1.82927
5 5K2M ADP 0.01896 0.40897 1.8315
6 4B9Z ACR 0.01395 0.40717 2.13415
7 2OAZ I96 0.01196 0.4159 2.43902
8 5A7V MAN 0.006234 0.40059 2.43902
9 4ZWP M44 0.01292 0.40226 2.7439
10 4CD6 IFM BMA 0.01141 0.40489 3.125
11 1UAS GLA 0.005219 0.4165 3.35366
12 5B25 4QJ 0.0109 0.40837 3.35366
13 1ELU PDA 0.01411 0.40881 3.65854
14 2E7F C2F 0.01328 0.40197 3.81679
15 2FB3 GTP 0.03749 0.40036 3.96341
16 5M12 7D0 0.001185 0.42682 4
17 1ZGD NAP 0.03613 0.4012 4.16667
18 3UXL CFI 0.04453 0.4075 4.26829
19 3A23 GAL 0.004775 0.41375 4.57317
20 3AYS CT3 0.01026 0.40251 4.57317
21 4Y24 TD2 0.01214 0.40152 5.84416
22 5MGD GLC GAL GAL 0.003075 0.44546 6.70732
23 4CU7 GIF 0.01137 0.40289 6.70732
24 5A5W GUO 0.04554 0.40609 7.11462
25 1QPR PPC 0.009197 0.42163 7.39437
26 1WKM MET 0.0009056 0.42464 7.45763
27 5T9C G3P 0.003761 0.4003 7.83582
28 5VSM MET 0.01761 0.40577 10.0629
29 4PMZ BXP 0.00000000000334 0.79671 42.5743
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