Receptor
PDB id Resolution Class Description Source Keywords
3B8X 1.7 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE H188N MUTANT WITH BOUND GDP-PEROSAMINE ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE COLITOSE PEROSAMINE O-ANTIGENPYRIDOXAL PHOSPHATE TRANSFERASE
Ref.: GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMO SUGAR SUBSTRATE IN THE ACTIVE SITE. J.BIOL.CHEM. V. 283 4295 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:674;
A:675;
A:676;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
G4M A:500;
B:500;
Valid;
Valid;
none;
none;
submit data
819.499 C24 H36 N7 O19 P3 Cc1c(...
NA A:669;
A:671;
A:672;
A:673;
B:666;
B:667;
B:668;
B:670;
Part of Protein;
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;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B8X 1.7 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE H188N MUTANT WITH BOUND GDP-PEROSAMINE ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE COLITOSE PEROSAMINE O-ANTIGENPYRIDOXAL PHOSPHATE TRANSFERASE
Ref.: GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMO SUGAR SUBSTRATE IN THE ACTIVE SITE. J.BIOL.CHEM. V. 283 4295 2008
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G4M; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 G4M 1 1
2 JB3 0.656489 0.928571
3 GDR 0.637795 0.916667
4 GFB 0.637795 0.916667
5 JB2 0.623077 0.916667
6 GDD 0.604651 0.916667
7 GDC 0.604651 0.916667
8 GKE 0.604651 0.916667
9 GDX 0.593985 0.904762
10 GPD 0.58209 0.885057
11 6CK 0.571429 0.873563
12 G1R 0.555556 0.892857
13 GP3 0.552846 0.904762
14 GKD 0.551471 0.916667
15 GDP 0.548387 0.880952
16 GTP 0.547619 0.880952
17 GNP 0.539062 0.860465
18 GSP 0.539062 0.840909
19 GNH 0.531746 0.870588
20 GCP 0.53125 0.860465
21 G 0.520325 0.869048
22 5GP 0.520325 0.869048
23 G2R 0.518797 0.872093
24 Y9Z 0.510949 0.886364
25 G3A 0.503597 0.904762
26 GMV 0.5 0.860465
27 G5P 0.5 0.904762
28 GTG 0.496403 0.895349
29 YGP 0.492754 0.863636
30 GPG 0.492647 0.916667
31 G2P 0.492424 0.872093
32 GAV 0.485075 0.850575
33 GP2 0.476923 0.872093
34 CAG 0.473684 0.846154
35 2MD 0.473333 0.815217
36 GDP MG 0.469697 0.818182
37 GDP AF3 0.467153 0.791209
38 GTP MG 0.466667 0.818182
39 GDP BEF 0.466165 0.8
40 ALF 5GP 0.466165 0.791209
41 FEG 0.463087 0.908046
42 ZGP 0.46 0.876405
43 GDP ALF 0.456522 0.791209
44 BEF GDP 0.455882 0.791209
45 U2G 0.453333 0.873563
46 NGD 0.453333 0.894118
47 GCP G 0.452555 0.827586
48 0O2 0.45 0.869048
49 JBT 0.449495 0.864583
50 2QR 0.447205 0.831461
51 FE9 0.44586 0.752475
52 MD1 0.443038 0.815217
53 G4P 0.442029 0.869048
54 GDP 7MG 0.438356 0.872093
55 G3D 0.437956 0.869048
56 CG2 0.437909 0.873563
57 TPG 0.4375 0.829787
58 G G 0.43662 0.870588
59 MGD 0.435897 0.815217
60 PGD 0.433962 0.842697
61 GMP 0.430894 0.797619
62 G1R G1R 0.419753 0.905882
63 DBG 0.419753 0.883721
64 I2C FE2 CMO CMO 0.40625 0.78125
65 G A A A 0.405063 0.882353
66 U A G G 0.402516 0.870588
67 3GP 0.401515 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 3b8x.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DVZ GLU 0.02524 0.41117 1.27389
2 2X5F PLP 0.01082 0.43014 1.28205
3 2FYF PLP 0.01089 0.43432 1.53846
4 4BA5 PXG 0.00007029 0.52327 1.79487
5 3OPT AKG 0.0408 0.40767 1.87668
6 1M32 PLP 0.01102 0.44086 2.18579
7 3IP5 ALA 0.02859 0.41789 2.24719
8 1VJO PLP 0.001051 0.46712 2.30769
9 4ZWP M44 0.01892 0.42595 2.5641
10 5G4J EXT 0.001583 0.45029 2.82051
11 5KGS 6SR 0.002517 0.41032 2.82051
12 3WCS MAN NAG 0.046 0.40491 3.14961
13 1JQN DCO 0.01941 0.41331 3.58974
14 4FL0 PLP 0.02139 0.41117 3.58974
15 4IY7 0JO 0.0003344 0.47679 3.84615
16 4IY7 KOU 0.0003511 0.47584 3.84615
17 2OAT PFM 0.002918 0.44191 3.84615
18 3K7S R52 0.01877 0.41781 3.91061
19 1DQN IMU 0.02461 0.41562 3.91304
20 3EI9 PL6 0.005708 0.41209 4.10256
21 2F5X ASP 0.03727 0.41032 4.16667
22 4E3Q PMP 0.0002005 0.51879 4.35897
23 3W9F I3P 0.02281 0.41549 4.61538
24 4UOX PLP 0.000231 0.50962 4.87179
25 1SFF IK2 0.0003935 0.47361 4.87179
26 4UOX PUT 0.002304 0.45081 4.87179
27 1JS3 PLP 142 0.002503 0.44116 4.87179
28 4UOX PLP PUT 0.003615 0.43754 4.87179
29 4P83 U5P 0.01535 0.42232 4.94506
30 4J8T DOG 0.01895 0.41027 5.10949
31 1FC4 AKB PLP 0.00112 0.45718 5.89744
32 2TPL HPP 0.001672 0.42842 5.89744
33 1PZM 5GP 0.04235 0.40306 6.16114
34 2Q8C AKG 0.0173 0.42727 6.53409
35 1TE2 PGA 0.01763 0.42705 7.07965
36 1HGX 5GP 0.01792 0.4229 7.10383
37 5E58 CPZ 0.00327 0.46601 7.17949
38 1Q8A HCS 0.04961 0.4031 7.17949
39 1UU1 PMP HSA 0.01413 0.40069 7.46269
40 1DJ9 KAM 0.0005288 0.48138 8.07292
41 5E95 GDP 0.01977 0.40284 8.24742
42 1K1Y MAL 0.03481 0.4047 8.46154
43 3KCG NTP 0.0398 0.40451 8.47458
44 2C5S AMP 0.01716 0.4239 10
45 1GCK ASP PLP 0.007326 0.41646 10.1299
46 2ZC0 PMP 0.001468 0.45589 11.0256
47 1A5V Y3 0.03723 0.40996 12.0253
48 2CJH AKG 0.001052 0.4671 12.8205
49 5X2Z 3LM 0.0003632 0.40542 12.8205
50 2R2N PMP 0.00363 0.44984 13.0769
51 2BES RES 0.02464 0.40808 13.3721
52 4JE5 PMP 0.03942 0.40111 13.5897
53 2Z9V PXM 0.001176 0.49095 14.1026
54 4R5Z PMP 0.007823 0.4091 14.1689
55 1QMG DMV 0.01447 0.43441 18.4615
56 2OGA PGU 0.00000000849 0.52617 27.9487
57 4ZAH T5K 0.00000000434 0.64378 29.4872
58 1B9I PXG 0.00000009205 0.50401 30.7692
59 5U23 TQP 0.00000001028 0.58054 30.8901
60 3NUB UD0 0.000000001208 0.64595 34.2618
61 5K8B PDG 0.0000000007096 0.56089 35.641
62 2PO3 T4K 0.000000002872 0.61436 36.6667
63 5W70 9YM 0.00000007604 0.49658 37.1795
64 4K2M O1G 0.000000005065 0.67698 37.9487
65 1MDZ DCS 0.0006611 0.45201 40
66 1MDZ PLP 0.0009828 0.44382 40
67 5W71 9YM 0.000002201 0.52014 40.2564
68 5W71 PLP 0.00000001477 0.49615 40.2564
69 1O69 X04 0.00004216 0.4117 41.0256
70 2FNU PMP UD1 0.000000001565 0.62821 41.3333
71 3FRK TQP 0.000000002625 0.60037 42.0912
72 3DR4 G4M 0.000000000008823 0.66589 47.4359
Pocket No.: 2; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3b8x.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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