Receptor
PDB id Resolution Class Description Source Keywords
5D9P 1.8 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PBGH5A, A GLYCOSIDE HYDROLASE FAMILY 5 FROM PREVOTELLA BRYANTII B14, IN COMPLEX WITH AN INHIBITORYB ROMOACETYLGLYCOSYLAMINE DERIVATIVE OF XXXG PREVOTELLA BRYANTII ENDO-BETA-GLUCANASE/ENDO-XYLOGLUCANASE GLYCOSYL HYDROLASE FMIXED ALPHA-BETA TIM BARREL HYDROLASE
Ref.: STRUCTURE-FUNCTION ANALYSIS OF A MIXED-LINKAGE BETA-GLUCANASE/XYLOGLUCANASE FROM KEY RUMINAL BACTE PREVOTELLA BRYANTII B14. J.BIOL.CHEM. 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:401;
A:401;
Part of Protein;
Invalid;
none;
none;
submit data
40.078 Ca [Ca+2...
NBG BGC BGC XYS BGC XYS XYS A:402;
A:409;
B:402;
B:409;
Invalid;
Valid;
Invalid;
Valid;
none;
none;
none;
none;
submit data
1103.98 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D9O 1.55 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PBGH5A, A GLYCOSIDE HYDROLASE FAMILY 5 FROM PREVOTELLA BRYANTII B14, E280A MUTANT IN COMPLEX WITH C ELLOTETRAOSE PREVOTELLA BRYANTII ENDO-BETA-GLUCANASE/ENDO-XYLOGLUCANASE GLYCOSYL HYDROLASE FMIXED ALPHA-BETA TIM BARREL HYDROLASE
Ref.: STRUCTURE-FUNCTION ANALYSIS OF A MIXED-LINKAGE BETA-GLUCANASE/XYLOGLUCANASE FROM KEY RUMINAL BACTE PREVOTELLA BRYANTII B14. J.BIOL.CHEM. 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5D9M - GLC BGC BGC XYS BGC XYS XYS n/a n/a
2 5D9N - BGC BGC BGC XYS BGC XYS XYS n/a n/a
3 5D9P - NBG BGC BGC XYS BGC XYS XYS n/a n/a
4 5D9O - BGC BGC BGC BGC n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5D9M - GLC BGC BGC XYS BGC XYS XYS n/a n/a
2 5D9N - BGC BGC BGC XYS BGC XYS XYS n/a n/a
3 5D9P - NBG BGC BGC XYS BGC XYS XYS n/a n/a
4 5D9O - BGC BGC BGC BGC n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5D9M - GLC BGC BGC XYS BGC XYS XYS n/a n/a
2 5D9N - BGC BGC BGC XYS BGC XYS XYS n/a n/a
3 5D9P - NBG BGC BGC XYS BGC XYS XYS n/a n/a
4 5D9O - BGC BGC BGC BGC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NBG BGC BGC XYS BGC XYS XYS; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 NBG BGC BGC XYS BGC XYS XYS 1 1
2 BGC BGC BGC XYS BGC XYS XYS 0.710843 0.744681
3 BGC BGC XYS BGC XYS BGC XYS 0.710843 0.744681
4 GLC BGC BGC XYS BGC XYS XYS 0.710843 0.744681
5 GLC BGC BGC BGC XYS BGC XYS XYS 0.670455 0.729167
6 GLC GLC BGC XYS BGC XYS 0.639535 0.744681
7 BGC BGC XYS BGC 0.635294 0.744681
8 BGC BGC BGC XYS BGC XYS XYS GAL GAL 0.630435 0.729167
9 BGC BGC XYS BGC BGC XYS XYS GAL GAL 0.630435 0.729167
10 BGC BGC XYS BGC XYS GAL 0.630435 0.729167
11 XYS BGC BGC XYS BGC XYS BGC BGC BGC 0.625 0.744681
12 XYS BGC BGC BGC BGC XYS BGC BGC BGC 0.625 0.744681
13 BGC BGC BGC XYS BGC BGC 0.625 0.744681
14 GLC BGC BGC XYS BGC XYS XYS GAL 0.621053 0.744681
15 BGC BGC XYS BGC GAL XYS BGC XYS GAL 0.621053 0.744681
16 GAL XYS XYS BGC BGC BGC XYS GAL BGC 0.621053 0.744681
17 GLC BGC BGC XYS BGC XYS XYS GAL GAL 0.621053 0.744681
18 GAL BGC BGC BGC XYS XYS 0.621053 0.744681
19 GLC GLC XYS XYS 0.609756 0.723404
20 BGC BGC BGC XYS BGC XYS GAL 0.578947 0.744681
21 GAL BGC BGC BGC XYS BGC XYS 0.578947 0.744681
22 GLO BGC BGC XYS BGC XYS XYS 0.57 0.765957
23 BGC BGC BGC XYS GAL 0.505263 0.744681
24 GAL BGC NAG GAL 0.458333 0.957447
25 BMA BMA BMA BMA GLA BMA GLA 0.457944 0.686275
26 GAL BGC BGC XYS 0.457447 0.744681
27 NAG NAG BMA MAN NAG 0.446429 0.851852
28 8VZ 0.436782 0.882353
29 GLC GLC GLC BGC 0.434783 0.702128
30 BMA BMA GLA BMA BMA 0.430108 0.702128
31 NAG BMA 0.422222 0.9
32 GLC GLC GLC GLC GLC GLC 0.413043 0.702128
33 G6S NAG 0.412371 0.737705
34 NAG MAN GAL MAN MAN NAG GAL 0.409091 0.9
35 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.405172 0.92
36 GAL NAG GAL 0.4 0.958333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D9O; Ligand: BGC BGC BGC BGC; Similar sites found: 55
This union binding pocket(no: 1) in the query (biounit: 5d9o.bio2) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Z48 NGA 0.04782 0.40957 1.13314
2 1XL8 152 0.0373 0.41365 1.69972
3 1DCP HBI 0.0105 0.42559 1.92308
4 3II1 BGC 0.00008938 0.56008 1.983
5 3AI0 PNW 0.002188 0.45863 2.26629
6 2NSX IFM 0.007788 0.43545 2.26629
7 3GNP SOG 0.001814 0.46264 2.54958
8 4IPN 1FT 0.008308 0.43404 2.54958
9 5W3Y ACO 0.03366 0.40749 2.84091
10 4J25 OGA 0.04775 0.40222 3.05677
11 4FFG 0U8 0.02266 0.41553 3.11615
12 2VRQ XYP XYP AHR 0.006072 0.43291 3.39943
13 1A99 PUT 0.04511 0.40561 3.48837
14 4LI4 AMP 0.02424 0.41801 3.67647
15 5GZK BGC 0.007019 0.43672 3.68272
16 4IF4 BEF 0.01896 0.43234 3.84615
17 3PDT ADP 0.01595 0.41607 4.72727
18 3HQP FDP 0.01921 0.41938 4.81586
19 1W9D SEH 0.005405 0.41834 4.81586
20 1Z17 ILE 0.0346 0.41499 4.94186
21 2VWA PTY 0.04749 0.41517 4.9505
22 3ZQ9 NOY BGC 0.006822 0.42008 5.09915
23 3L24 GOA 0.04809 0.41327 5.09915
24 4UCF GLA 0.03677 0.40468 5.38244
25 3OGV PTQ 0.01767 0.41047 5.94901
26 5W3X ACO 0.04646 0.4072 6.25
27 4UOZ GLA 0.01255 0.43322 6.51558
28 5AYI BGC 0.000542 0.5116 6.79887
29 3PTQ NFG 0.001656 0.46011 6.93069
30 4RKC PMP 0.01414 0.41866 7.36544
31 5MGD GLC GAL GAL 0.00103 0.45346 7.93201
32 1P4A PCP 0.009008 0.42113 8.07018
33 3CYI ATP 0.02289 0.42492 8.18182
34 3HY2 ATP 0.02848 0.41428 8.18182
35 1IPC MGP 0.01833 0.42879 8.29493
36 2WMC MGP 0.04318 0.4134 8.98876
37 4CD6 IFM BMA 0.01428 0.4347 9.0625
38 3KP6 SAL 0.0212 0.43608 9.27152
39 5BXV MGP 0.002099 0.48148 9.375
40 1ECE BGC BGC BGC BGC 0.01281 0.40472 9.63173
41 2OYL IDC 0.006663 0.42385 9.91501
42 4RW3 PLM 0.01523 0.40688 11.5894
43 5GNX BGC 0.0003463 0.5257 12.4646
44 3AXX CBI 0.009573 0.40203 13.3144
45 2E40 LGC 0.0002076 0.53846 13.881
46 4PTX BGC 0.001676 0.46433 14.1643
47 4JIE BMA 0.001671 0.48724 19.5467
48 4U5I BXP 0.00002372 0.5935 36.8272
49 3RJY GLC 0.000629 0.49214 36.875
50 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.0000002348 0.66276 39.3768
51 3AYS CT3 0.0000002216 0.68376 41.6431
52 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.0000007939 0.61982 42.7762
53 4W88 GAL BGC BGC BGC XYS XYS 0.0000115 0.57069 43.8235
54 4YHG CT3 0.00000159 0.61294 44.7592
55 4YZT BGC BGC BGC BGC 0.0000004247 0.65905 45.3258
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