Receptor
PDB id Resolution Class Description Source Keywords
2VGD 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF ENVIRONMENTAL ISOLATED GH11 IN COMPLEX WITH XYLOBIOSE AND FERULOYL-ARABINO-XYLOTRIOSE ESCHERICHIA COLI GLYCOSIDE HYDROLASE XYLANASE BETA JELLY ROLL HYDROLASE
Ref.: UNDERSTANDING THE STRUCTURAL BASIS FOR SUBSTRATE AND INHIBITOR RECOGNITION IN EUKARYOTIC GH11 XYLANASES. J.MOL.BIOL. V. 375 1293 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1201;
A:1202;
A:1203;
A:1204;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA A:1196;
Part of Protein;
none;
submit data
22.99 Na [Na+]
XYP XYP A:1205;
Valid;
none;
submit data
282.245 n/a O(C1O...
XYP XYP XYP FX3 A:1198;
Valid;
none;
submit data
722.646 n/a O(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VGD 1.8 Å EC: 3.2.1.8 CRYSTAL STRUCTURE OF ENVIRONMENTAL ISOLATED GH11 IN COMPLEX WITH XYLOBIOSE AND FERULOYL-ARABINO-XYLOTRIOSE ESCHERICHIA COLI GLYCOSIDE HYDROLASE XYLANASE BETA JELLY ROLL HYDROLASE
Ref.: UNDERSTANDING THE STRUCTURAL BASIS FOR SUBSTRATE AND INHIBITOR RECOGNITION IN EUKARYOTIC GH11 XYLANASES. J.MOL.BIOL. V. 375 1293 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 2VGD - XYP XYP n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 2VGD - XYP XYP n/a n/a
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3LGR - PDC C7 H5 N O4 c1cc(nc(c1....
2 4HK9 - XYP XYP XYP n/a n/a
3 4HK8 - XYP XYP XYP XYP XYP XYP n/a n/a
4 4HKW - XYP XYP TRS n/a n/a
5 2VGD - XYP XYP n/a n/a
6 1BCX - XYP XYP n/a n/a
7 2QZ3 - XYP XYP XYP n/a n/a
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 FX3; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP XYP XYP FX3 1 1
2 XYP XYP AHR FER 0.833333 1
3 XYP AHR XYP XYP 0.542056 0.795455
4 XYP XYP XYP AHR 0.542056 0.795455
5 XYS XYP AHR XYP 0.542056 0.795455
6 AHR XYS XYP XYP XYP 0.442478 0.795455
7 AHR XYP XYP XYP 0.401709 0.795455
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VGD; Ligand: XYP XYP; Similar sites found: 53
This union binding pocket(no: 1) in the query (biounit: 2vgd.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ST0 GTG 0.03431 0.40105 0.917431
2 1LBF 137 0.01558 0.42074 1.37615
3 4QTB 38Z 0.02789 0.41068 1.83486
4 4YMH SAH 0.02193 0.40637 1.83486
5 1SU2 ATP 0.01136 0.40886 1.88679
6 1LVG 5GP 0.01449 0.40968 2.0202
7 4WAS COO 0.01027 0.42151 2.29358
8 5KXQ GDP 0.003653 0.44966 2.75229
9 5KY3 GFB 0.01063 0.43704 2.75229
10 5KY4 GDP 0.005787 0.43393 2.75229
11 5UXH GFB 0.01416 0.41727 2.75229
12 3WLE NAD 0.04966 0.40816 2.75229
13 4BJ8 BTN 0.01824 0.40608 3.1746
14 4TQ3 GPP 0.01471 0.40259 3.21101
15 5F7V GLC GLC GLC GLC 0.01958 0.40621 3.66972
16 2GJ5 VD3 0.02716 0.40549 3.7037
17 2VVT DGL 0.005119 0.43481 4.12844
18 5DWQ SFG 0.02319 0.4075 4.12844
19 3GDN HBX 0.04472 0.42071 4.58716
20 5DM1 5D7 0.03238 0.41784 4.58716
21 5DM1 SAH 0.0313 0.41784 4.58716
22 4GQP B40 0.004325 0.4253 5.04587
23 5BV3 M7G 0.01488 0.41189 5.04587
24 4CS4 ANP 0.01958 0.41377 5.50459
25 4CS4 AXZ 0.02401 0.41377 5.50459
26 5G09 6DF 0.02523 0.40292 5.9633
27 4Q3F TLA 0.003992 0.41815 5.98291
28 3AFN NAP 0.0493 0.40841 6.20155
29 1JIF CU BLM 0.02038 0.40442 6.55738
30 4EO3 FMN 0.02615 0.40483 6.88073
31 1VBO MAN MAN MAN 0.009059 0.40205 6.88073
32 5C9J STE 0.01608 0.41022 7.07071
33 5CMK GLU 0.02167 0.41205 7.33945
34 2BJK NAD 0.03173 0.40993 7.33945
35 1NJR XYL 0.02674 0.40695 7.33945
36 3EW2 BTN 0.01507 0.40942 7.40741
37 1MJJ HAL 0.007378 0.43116 7.48899
38 4EKV BTN 0.02025 0.40224 7.54717
39 1WBI BTN 0.02178 0.40167 7.75194
40 5A8R TP7 0.03369 0.40584 8.25688
41 1SWG BTN 0.01378 0.41348 8.59375
42 5N1Q TP7 0.01219 0.41285 8.7156
43 2YBQ SAH 0.01088 0.41135 8.7156
44 4KIB 56D 0.01007 0.40772 8.7156
45 4ITU 1HS 0.0287 0.41829 9.17431
46 3MJE NDP 0.02573 0.4087 9.17431
47 3ZY6 GFB 0.01396 0.42138 9.63303
48 5KY9 GDP 0.005005 0.44305 10
49 1JCM 137 0.01356 0.41063 10.0917
50 5NCF 8T5 0.003287 0.43192 10.6195
51 4CM8 IZ9 0.01302 0.40242 11.4679
52 2Z3U CRR 0.03372 0.40622 14.6789
53 5KY5 GDP 0.004569 0.44398 22.5
Pocket No.: 2; Query (leader) PDB : 2VGD; Ligand: XYP XYP XYP FX3; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 2vgd.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PIO SAH 0.02779 0.40206 3.21101
2 4DP3 NDP 0.0452 0.40044 3.21101
3 4DP3 MMV 0.0452 0.40044 3.21101
4 1Z45 GAL 0.01499 0.40604 3.66972
5 4MP8 NAD 0.01239 0.42254 5.04587
6 1S1D GP2 0.009125 0.40381 5.50459
7 1EM6 CP4 0.04522 0.42416 5.9633
8 5U98 1KX 0.01174 0.43874 7.07071
9 2AXR ABL 0.005018 0.43379 8.25688
10 3STK PLM 0.01359 0.41628 8.33333
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