Receptor
PDB id Resolution Class Description Source Keywords
2GMS 1.8 Å EC: 4.-.-.- E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE WITH BOUND HYDRATED PLP ESCHERICHIA COLI COLITOSE 0-ANTIGEN ASPARTATE AMINOTRANSFERASE PLP DEOXYSUGAR
Ref.: THE STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE: A UNIQUE COENZYME B6-DEPENDENT ENZYME. PROTEIN SCI. V. 15 2093 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:403;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
P0P A:400;
B:401;
Valid;
Valid;
none;
none;
submit data
265.157 C8 H12 N O7 P Cc1c(...
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: P0P; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 P0P 1 1
2 PLR 0.557692 0.895833
3 PLP 0.527273 0.916667
4 PXP 0.517857 0.9
5 PZP 0.517857 0.88
6 PMP 0.508772 0.8
7 GT1 0.5 0.830189
8 EPC 0.461538 0.826923
9 PLG 0.454545 0.75
10 IN5 0.454545 0.758621
11 2BK 0.442857 0.793103
12 TLP 0.442857 0.793103
13 2BO 0.442857 0.793103
14 AN7 0.439394 0.88
15 PDD 0.434783 0.762712
16 PP3 0.434783 0.762712
17 PDA 0.434783 0.762712
18 EXT 0.432836 0.767857
19 FOO 0.432836 0.814815
20 KOU 0.428571 0.836364
21 33P 0.428571 0.745763
22 PL6 0.424658 0.785714
23 PLS 0.422535 0.779661
24 4LM 0.42029 0.785714
25 0JO 0.42029 0.77193
26 CBA 0.418919 0.754098
27 PFM 0.418919 0.77193
28 C6P 0.416667 0.75
29 PPD 0.416667 0.75
30 MPM 0.414286 0.781818
31 P1T 0.414286 0.714286
32 PY5 0.410959 0.703125
33 IK2 0.408451 0.714286
34 6DF 0.405405 0.811321
35 PMH 0.402778 0.642857
36 P3D 0.402778 0.704918
37 5PA 0.402778 0.714286
38 HCP 0.402778 0.741379
39 N5F 0.402597 0.714286
40 Z98 0.4 0.721311
41 PGU 0.4 0.725806
42 ILP 0.4 0.737705
43 PDG 0.4 0.725806
44 7XF 0.4 0.725806
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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