Receptor
PDB id Resolution Class Description Source Keywords
5K8B 2.15 Å EC: 2.6.1.109 X-RAY STRUCTURE OF KDNA, 8-AMINO-3,8-DIDEOXY-ALPHA-D-MANNO- OCTULOSONATE TRANSAMINASE, FROM SHEWANELLA ONEIDENSIS IN THO F THE EXTERNAL ALDIMINE WITH PLP AND GLUTAMATE SHEWANELLA ONEIDENSIS (STRAIN MR-1) TRANSAMINASE 8-AMINO-3 8-DIDEOXY-D-MANNO-OCTULOSONIC ACIDSUGAR TRANSFERASE
Ref.: STRUCTURES OF KDNB AND KDNA FROM SHEWANELLA ONEIDEN ENZYMES IN THE FORMATION OF 8-AMINO-3,8-DIDEOXY-D-MANNO-OCTULOSONIC ACID. BIOCHEMISTRY V. 55 4485 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PDG A:501;
B:501;
C:501;
D:501;
Valid;
Invalid;
Valid;
Valid;
none;
none;
none;
none;
submit data
378.272 C13 H19 N2 O9 P Cc1c(...
CL D:502;
A:503;
C:503;
B:502;
A:502;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
NA C:502;
Invalid;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K8B 2.15 Å EC: 2.6.1.109 X-RAY STRUCTURE OF KDNA, 8-AMINO-3,8-DIDEOXY-ALPHA-D-MANNO- OCTULOSONATE TRANSAMINASE, FROM SHEWANELLA ONEIDENSIS IN THO F THE EXTERNAL ALDIMINE WITH PLP AND GLUTAMATE SHEWANELLA ONEIDENSIS (STRAIN MR-1) TRANSAMINASE 8-AMINO-3 8-DIDEOXY-D-MANNO-OCTULOSONIC ACIDSUGAR TRANSFERASE
Ref.: STRUCTURES OF KDNB AND KDNA FROM SHEWANELLA ONEIDEN ENZYMES IN THE FORMATION OF 8-AMINO-3,8-DIDEOXY-D-MANNO-OCTULOSONIC ACID. BIOCHEMISTRY V. 55 4485 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5K8B - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5K8B - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5K8B - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PDG; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 PGU 1 1
2 PDG 1 1
3 QLP 0.865672 0.938462
4 N5F 0.84058 0.983871
5 PY5 0.820895 0.9375
6 7XF 0.797101 0.967742
7 PPD 0.779412 0.967213
8 PY6 0.774648 0.909091
9 PLS 0.764706 0.935484
10 ORX 0.763889 0.952381
11 C6P 0.753623 0.935484
12 PE1 0.753425 0.952381
13 PL4 0.733333 0.952381
14 76U 0.702703 0.952381
15 PDD 0.685714 0.888889
16 PP3 0.685714 0.888889
17 PDA 0.685714 0.888889
18 2BK 0.666667 0.888889
19 TLP 0.666667 0.888889
20 2BO 0.666667 0.888889
21 AQ3 0.658537 0.878788
22 ILP 0.653333 0.890625
23 EA5 0.649351 0.953125
24 IN5 0.619718 0.857143
25 PLG 0.619718 0.935484
26 KAM 0.609756 0.921875
27 IK2 0.608108 0.892308
28 PPE 0.589744 0.983871
29 CBA 0.589744 0.848485
30 PLA 0.584416 0.907692
31 PMG 0.582278 0.938462
32 P1T 0.573333 0.892308
33 5PA 0.558442 0.921875
34 33P 0.545455 0.84375
35 PSZ 0.53012 0.785714
36 PXP 0.529412 0.774194
37 HEY 0.518072 0.9375
38 3LM 0.511905 0.826087
39 PLP ALO 0.5 0.84375
40 PMP 0.5 0.83871
41 PMH 0.5 0.688312
42 PXG 0.494253 0.846154
43 RW2 0.494253 0.865672
44 7TS 0.493976 0.696203
45 GT1 0.492958 0.69697
46 PL2 0.488095 0.823529
47 DCS 0.488095 0.75
48 PL6 0.481928 0.825397
49 9YM 0.454545 0.820895
50 PL8 0.43956 0.819444
51 CAN PLP 0.438202 0.907692
52 1D0 0.431579 0.838235
53 7B9 0.430108 0.855072
54 PLR 0.428571 0.68254
55 PPG 0.423913 0.892308
56 PLP 2KZ 0.423529 0.815385
57 KOU 0.416667 0.8125
58 0JO 0.409639 0.731343
59 Z98 0.409091 0.846154
60 PUS 0.402174 0.702703
61 P0P 0.4 0.725806
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found: 115
This union binding pocket(no: 1) in the query (biounit: 5k8b.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1FC4 AKB PLP 0.0004755 0.45659 0.997506
2 1U08 PLP 0.0001544 0.50586 1.29534
3 2HHP FLC 0.02125 0.45324 1.48883
4 3A70 NPO 0.001487 0.41661 1.48883
5 5AHO TLA 0.005875 0.45302 1.78571
6 1AJ8 CIT 0.02523 0.40751 1.88679
7 4RM0 FUC NDG GAL 0.02902 0.40581 1.89873
8 5GVL PLG 0.0008045 0.45799 1.98511
9 5GVL GI8 0.0008045 0.45799 1.98511
10 2X5F PLP 0.001748 0.45426 1.98511
11 5WYF ILP 0.0006464 0.44654 1.98511
12 4ZM4 PLP 0.0001036 0.50185 2.23325
13 1DFO PLG 0.00009287 0.46257 2.23325
14 5IWQ PLP 0.005647 0.4249 2.23325
15 4ZM4 P3B 0.002221 0.42359 2.23325
16 2Z8L NAG FUC SIA GAL 0.008544 0.4283 2.40385
17 1JS3 PLP 142 0.004197 0.41524 2.48139
18 2HOX P1T 0.007649 0.40382 2.48139
19 5LUN OGA 0.0232 0.40715 2.55682
20 2P1E LAC 0.01739 0.4202 2.57235
21 1K4M CIT 0.02304 0.41748 2.8169
22 3FQ8 PMP 0.0001752 0.46397 2.97767
23 4WXG 2BO 0.0001969 0.45301 2.97767
24 4MXP DB4 0.006986 0.41644 3.04878
25 4ZSY RW2 0.0005588 0.44516 3.22581
26 3R75 PYR 0.01559 0.41767 3.22581
27 1MLY ACZ PLP 0.00166 0.40703 3.22581
28 4UOX PLP 0.00009276 0.51021 3.47395
29 2ZC0 PMP 0.0002286 0.47533 3.47395
30 4UOX PUT 0.001954 0.43791 3.47395
31 4UOX PLP PUT 0.005286 0.41441 3.47395
32 3PDB PMP 0.00005992 0.51927 3.49127
33 3PD6 PMP 0.0001159 0.51197 3.49127
34 1VPE 3PG 0.02354 0.40555 3.51759
35 1W6F ISZ 0.02197 0.40711 3.59712
36 2CFC KPC 0.02587 0.4051 3.6
37 2OAT PFM 0.002492 0.42902 3.72208
38 2FYF PLP 0.007118 0.42891 3.76884
39 3CQ5 PMP 0.004644 0.44336 4.06504
40 1Z17 ILE 0.02148 0.41118 4.06977
41 5EOO CIT 0.01053 0.42764 4.15094
42 4HZ0 1AV 0.02359 0.40158 4.22535
43 4GN8 ASO 0.01153 0.41835 4.34783
44 3VP6 HLD 0.001926 0.42262 4.4665
45 5DJ3 5DK 0.002218 0.40468 4.52128
46 4RF7 ARG 0.02524 0.41451 4.71464
47 5EGH PC 0.01879 0.4036 4.71464
48 4BA5 PXG 0.00003424 0.51805 4.96278
49 5G09 6DF 0.0008897 0.4406 4.96278
50 3BWN PMP 0.0007396 0.46713 5.11509
51 3BWN PMP PHE 0.005143 0.40471 5.11509
52 4JE5 PLP 0.01234 0.41261 5.21092
53 4JE5 PMP 0.01259 0.41219 5.21092
54 5NE2 DGL 0.01915 0.40362 5.39568
55 3WGC PLG 0.00008592 0.49982 5.57185
56 4CP9 GAL CN8 0.01775 0.41321 5.78512
57 1PMO PLR 0.001565 0.45157 5.95534
58 1WYV PLP AOA 0.001872 0.43457 5.95534
59 5A7V MAN 0.03159 0.40118 6.4433
60 4ADC PLP 0.00153 0.41734 6.45161
61 2OVR SER LEU ILE PRO TPO PRO ASP LYS 0.01843 0.41392 6.71141
62 4IYO 0JO 0.0004798 0.45208 6.80101
63 4IY7 KOU 0.0005024 0.45122 6.80101
64 4IY7 0JO 0.0005698 0.44889 6.80101
65 1ELU PDA 0.006467 0.40701 6.92308
66 5DDW 5B6 0.001136 0.43223 7.07457
67 2VPY PCI 0.009152 0.42813 7.17949
68 5G4J EXT 0.0007502 0.44793 7.19603
69 5X30 4LM 0.0001094 0.48962 7.53769
70 5X30 7XF 0.0001314 0.48099 7.53769
71 5X2Z 3LM 0.0003919 0.45316 7.53769
72 1AJS PLA 0.000751 0.43784 7.69231
73 2WK9 PLG 0.0000737 0.49381 7.96915
74 2WK9 PLP 0.0001151 0.48235 7.96915
75 4AOA IK2 0.000155 0.48814 8.933
76 2Z9I GLY ALA THR VAL 0.009595 0.43227 9.25926
77 4RKC PMP 0.000278 0.48184 9.29648
78 1XXR MAN 0.01283 0.42142 9.31677
79 4E3Q PMP 0.0000346 0.53765 9.42928
80 4R5Z PMP 0.004193 0.40524 9.80926
81 2R2N PMP 0.001141 0.45813 10.4218
82 1UU1 PMP HSA 0.005702 0.40283 10.4478
83 3E2Y PMP 0.000331 0.48381 10.4878
84 4UHO PLP 0.0004163 0.49738 10.67
85 1GCK ASP PLP 0.001405 0.43211 12.1588
86 4WGF HX2 0.04364 0.40042 12.1951
87 1GDE GLU PLP 0.00625 0.40766 12.8535
88 1SFF IK2 0.0003023 0.46067 12.9032
89 1XI9 PLP 0.01828 0.40823 13.5468
90 2R5E QLP 0.001944 0.42607 14.1439
91 2R5C C6P 0.001814 0.41254 14.1439
92 1M32 PLP 0.002318 0.46011 14.2077
93 1LW4 TLP 0.0001995 0.44337 15.2738
94 1LW4 PLP 0.0003559 0.42168 15.2738
95 1ZC9 PMP 0.0003825 0.46072 15.6328
96 4FL0 PLP 0.003615 0.43418 15.8809
97 3IX1 NFM 0.0165 0.41486 17.5497
98 1DJ9 KAM 0.00006779 0.50452 20.5729
99 4K2M O1G 0.0000000001111 0.7167 29.5285
100 2PO3 T4K 0.000000001984 0.5454 31.0174
101 1O69 X04 0.0000001988 0.4239 31.7259
102 2FNU PMP UD1 0.0000000003661 0.55373 32
103 3DR4 G4M 0.0000000004136 0.53627 32.9923
104 5W70 9YM 0.000000000191 0.7259 34.4913
105 5W71 9YM 0.00000000115 0.71736 34.4913
106 5W71 PLP 0.000000000009419 0.70788 34.4913
107 4ZAH T5K 0.000000005052 0.58747 34.596
108 1B9I PXG 0.00001518 0.54631 34.7938
109 3NUB UD0 0.0000000003916 0.59594 34.8189
110 2OGA PGU 0.00000000314 0.64726 35.3383
111 3B8X G4M 0.0000000007096 0.56089 35.641
112 5U23 TQP 0.000000003367 0.6778 39.7906
113 1MDZ PLP 0.00000019 0.50134 41.4392
114 1MDZ DCS 0.0000002112 0.49297 41.4392
115 3FRK TQP 0.000000001064 0.58155 41.555
Pocket No.: 2; Query (leader) PDB : 5K8B; Ligand: PDG; 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: 5k8b.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5k8b.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found: 7
This union binding pocket(no: 4) in the query (biounit: 5k8b.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2F5X ASP 0.02456 0.40587 1.92308
2 5TDC NMM ILE PHE SER 0.02484 0.40343 2.63158
3 4ZYB 4SQ 0.0172 0.40168 3.73134
4 4JCA CIT 0.00684 0.4027 4.19162
5 5N18 8HZ 0.03449 0.40053 6.42202
6 5T7I LAT NAG GAL 0.01923 0.41214 6.45161
7 5U75 SIA GAL NDG FUC 0.0162 0.41344 7.14286
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