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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
164.157 n/a O(C)C...
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 (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 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VBR; Ligand: XYS XYP; Similar sites found with APoc: 67
This union binding pocket(no: 1) in the query (biounit: 1vbr.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3ETH ATP 0.914634
2 5M67 3D1 1.21951
3 5M67 NAD 1.21951
4 5M67 ADE 1.21951
5 3G3N TC8 1.57233
6 4Y2B EPK 1.82927
7 4U5I BXP 1.82927
8 2R8Q IBM 1.82927
9 4FFG 0U8 1.82927
10 5K2M ADP 1.8315
11 4B9Z ACR 2.13415
12 4CQB MLI 2.43902
13 5A7V MAN 2.43902
14 2OAZ I96 2.43902
15 3VDB 149 2.43902
16 1M5W DXP 2.46914
17 5VOP C2F 2.7027
18 4ZWP M44 2.7439
19 3S5W ONH 2.80778
20 2I6U NVA 2.9316
21 6C7D EOJ 3.04878
22 4CD6 IFM BMA 3.125
23 1M9H NAD 3.23741
24 2YFO GLA 3.35366
25 2YFO GAL 3.35366
26 1UAS GLA 3.35366
27 5B25 4QJ 3.35366
28 3VPB ADP 3.5461
29 1LBF 137 3.64372
30 1ELU PDA 3.65854
31 3OYW TDG 3.73134
32 2E7F C2F 3.81679
33 4AVV CD 3.92157
34 2WQP WQP 3.96341
35 2FB3 GTP 3.96341
36 6GVD FDK 4
37 1QFT HSM 4
38 1ZGD NAP 4.16667
39 3UXL CFI 4.26829
40 1GYM MYG 4.36242
41 3A23 GAL 4.57317
42 5HSS 64Z 4.57317
43 4O1F THG 4.82759
44 5NN6 MIG 5.4878
45 4Y24 TD2 5.84416
46 3WG6 NDP 6.18893
47 3V4S ADP 6.40244
48 5MGD GLC GAL GAL 6.70732
49 4CU7 GIF 6.70732
50 3R1Z ALA DGL 6.70732
51 5A5W GUO 7.11462
52 1QPR PPC 7.39437
53 1WKM MET 7.45763
54 3OND NAD 7.58197
55 3OND ADN 7.58197
56 5GNX BGC 7.62195
57 5T9C G3P 7.83582
58 5VSM MET 10.0629
59 6D61 4AA 10.2564
60 2ZJ1 ARJ 11.5854
61 2ZJ1 NAD 11.5854
62 4O9S 2RY 12.093
63 5H9O GLC 12.5
64 5Y72 DST 12.5
65 4S1B 2BA 13.5135
66 2XN2 GLA 16.4634
67 4PMZ BXP 42.5743
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