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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: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PDG 1 1
2 PGU 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 LPI 0.785714 0.895522
8 PPD 0.779412 0.967213
9 PY6 0.774648 0.909091
10 PLS 0.764706 0.935484
11 ORX 0.763889 0.952381
12 C6P 0.753623 0.935484
13 PE1 0.753425 0.952381
14 PL4 0.733333 0.952381
15 76U 0.702703 0.952381
16 PDA 0.685714 0.888889
17 PDD 0.685714 0.888889
18 PP3 0.685714 0.888889
19 TLP 0.666667 0.888889
20 2BK 0.666667 0.888889
21 2BO 0.666667 0.888889
22 AQ3 0.658537 0.878788
23 ILP 0.653333 0.890625
24 EA5 0.649351 0.953125
25 PLG 0.619718 0.935484
26 IN5 0.619718 0.857143
27 KAM 0.609756 0.921875
28 IK2 0.608108 0.892308
29 PPE 0.589744 0.983871
30 CBA 0.589744 0.848485
31 PLA 0.584416 0.907692
32 PMG 0.582278 0.938462
33 P1T 0.573333 0.892308
34 5PA 0.558442 0.921875
35 33P 0.545455 0.84375
36 PSZ 0.53012 0.785714
37 PXP 0.529412 0.774194
38 HEY 0.518072 0.9375
39 3LM 0.511905 0.826087
40 PMH 0.5 0.688312
41 PMP 0.5 0.83871
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 DCS 0.488095 0.75
47 PL2 0.488095 0.823529
48 PL6 0.481928 0.825397
49 9YM 0.454545 0.820895
50 PL8 0.43956 0.819444
51 CAN PLP 0.433333 0.893939
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 F0G 0.421687 0.75
58 KOU 0.416667 0.8125
59 0JO 0.409639 0.731343
60 Z98 0.409091 0.846154
61 RMT 0.404255 0.779412
62 PUS 0.402174 0.702703
63 FEV 0.4 0.705882
64 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 with APoc: 184
This union binding pocket(no: 1) in the query (biounit: 5k8b.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1FC4 AKB PLP 0.997506
2 6MVU K4V 1.24069
3 1U08 PLP 1.29534
4 2HHP FLC 1.48883
5 3A70 NPO 1.48883
6 4S00 AKR 1.73697
7 5AHO TLA 1.78571
8 1AJ8 CIT 1.88679
9 4RM0 FUC NDG GAL 1.89873
10 2X5F PLP 1.98511
11 5GVL PLG 1.98511
12 5GVL GI8 1.98511
13 5WYF ILP 1.98511
14 6CBO DOW 1.98511
15 1TOI HCI 2.0202
16 5WBF LAC 2.22222
17 4ZM4 PLP 2.23325
18 1DFO PLG 2.23325
19 5IWQ PLP 2.23325
20 5LXB 7A9 2.23325
21 3BS8 PMP 2.23325
22 4ZM4 P3B 2.23325
23 6FYQ PLP 2.23325
24 1GEX PLP HSA 2.24719
25 2ZYJ PGU 2.267
26 2Z8L NAG FUC SIA GAL 2.40385
27 1JS3 PLP 142 2.48139
28 2HOX P1T 2.48139
29 3EI9 PL6 2.48139
30 5LUN OGA 2.55682
31 2P1E LAC 2.57235
32 2JBH 5GP 2.66667
33 2CJH AKG 2.72953
34 1K4M CIT 2.8169
35 3FQ8 PMP 2.97767
36 4WXG 2BO 2.97767
37 4MXP DB4 3.04878
38 4ZSY RW2 3.22581
39 3R75 PYR 3.22581
40 2ZUX RAM 3.22581
41 1MLY ACZ PLP 3.22581
42 5DNC ASN 3.22581
43 5YKT PMP 3.2538
44 2HFK E4H 3.44828
45 4UOX PLP 3.47395
46 6CD1 PLS 3.47395
47 6CD1 PLG 3.47395
48 2ZC0 PMP 3.47395
49 4UOX PUT 3.47395
50 5W19 9TD 3.47395
51 4UOX PLP PUT 3.47395
52 2FN1 PYR 3.47395
53 3PDB PMP 3.49127
54 3PD6 PMP 3.49127
55 1VPE 3PG 3.51759
56 1W6F ISZ 3.59712
57 2CFC KPC 3.6
58 2OAT PFM 3.72208
59 1M7Y PPG 3.72208
60 1M1B SPV 3.72881
61 2FYF PLP 3.76884
62 5W6Y TRP 3.79747
63 4LS3 HIS 3.9039
64 3UCJ AZM 3.97022
65 3CQ5 PMP 4.06504
66 1Z17 ILE 4.06977
67 1LC8 33P 4.12088
68 5EOO CIT 4.15094
69 4HZ0 1AV 4.22535
70 4GN8 ASO 4.34783
71 3VP6 HLD 4.4665
72 6C92 EQJ 4.52128
73 6C8T EQJ 4.52128
74 4ZUL UN1 4.71464
75 4RF7 ARG 4.71464
76 5EGH PC 4.71464
77 2CHT TSA 4.72441
78 1U26 IHS 4.74777
79 3ZRR PXG 4.94792
80 4BA5 PXG 4.96278
81 5G09 6DF 4.96278
82 3BWN PMP 5.11509
83 3BWN PMP PHE 5.11509
84 4JE5 PLP 5.21092
85 4JE5 PMP 5.21092
86 6DND PLP 5.21092
87 5NE2 DGL 5.39568
88 3WGC PLG 5.57185
89 5UIV TMP 5.72687
90 4CP9 GAL CN8 5.78512
91 2PEL LBT 5.9322
92 1PMO PLR 5.95534
93 1WYV PLP AOA 5.95534
94 2HVW DCP 5.97826
95 4HVK PMP 6.28272
96 1VJO PLP 6.36132
97 5A7V MAN 6.4433
98 4ADC PLP 6.45161
99 2OVR SER LEU ILE PRO TPO PRO ASP LYS 6.71141
100 4IY7 KOU 6.80101
101 4IYO 0JO 6.80101
102 4IY7 0JO 6.80101
103 1ELU PDA 6.92308
104 5DDW 5B6 7.07457
105 2VPY PCI 7.17949
106 5G4J EXT 7.19603
107 4P8K 38C 7.29167
108 4P8K FAD 7.29167
109 3NIP 16D 7.36196
110 5TXR PLP 7.44417
111 4LNL 2BO 7.50751
112 4LNL 2BK 7.50751
113 4LNL PLG 7.50751
114 5X2Z 3LM 7.53769
115 5X30 7XF 7.53769
116 5X30 4LM 7.53769
117 1AJS PLA 7.69231
118 3A8U PLP 7.94045
119 2WK9 PLG 7.96915
120 2WK9 PLP 7.96915
121 3BGD PM6 8.43672
122 1FHW I5P 8.52713
123 1E5F PLP 8.933
124 4AOA IK2 8.933
125 1OXO IK2 8.97756
126 2Z9I GLY ALA THR VAL 9.25926
127 3O03 GCO 9.27835
128 4RKC PMP 9.29648
129 1XXR MAN 9.31677
130 4E3Q PMP 9.42928
131 4B98 PXG 9.42928
132 4R5Z PMP 9.80926
133 4R5Z SIN 9.80926
134 2R2N KYN 10.4218
135 2R2N PMP 10.4218
136 1UU1 PMP HSA 10.4478
137 5VEQ PMP 10.4623
138 4UHO PLP 10.67
139 4M2K PLP 10.9181
140 6CBN OZY 10.9589
141 1CL2 PPG 11.1392
142 6CI9 F3V 11.1969
143 5NM7 GLY 11.2782
144 1GCK ASP PLP 12.1588
145 4WGF HX2 12.1951
146 1GDE GLU PLP 12.8535
147 1SFF IK2 12.9032
148 5KGS 6SR 13.3995
149 1XI9 PLP 13.5468
150 2R5C C6P 14.1439
151 2R5E QLP 14.1439
152 1M32 PLP 14.2077
153 2Z9V PXM 14.5408
154 1JA9 PYQ 14.5985
155 1LW4 TLP 15.2738
156 1LW4 PLP 15.2738
157 5M3Z NLE 15.3266
158 5M3Z PY6 15.3266
159 5M3Z PLP 15.3266
160 1ZC9 PMP 15.6328
161 4FL0 PLP 15.8809
162 3IX1 NFM 17.5497
163 2TPL HPP 18.8586
164 6ECG PM9 19.1067
165 2XBN PMP 19.8511
166 1DJ9 KAM 20.5729
167 4K2M O1G 29.5285
168 2PO3 T4K 31.0174
169 1O69 X04 31.7259
170 2FNU PMP UD1 32
171 3DR4 G4M 32.9923
172 5W71 9YM 34.4913
173 5W71 PLP 34.4913
174 5W70 9YM 34.4913
175 6EWR PMP 34.4913
176 4ZAH T5K 34.596
177 1B9I PXG 34.7938
178 3NUB UD0 34.8189
179 2OGA PGU 35.3383
180 3B8X G4M 35.641
181 5U23 TQP 39.7906
182 1MDZ PLP 41.4392
183 1MDZ DCS 41.4392
184 3FRK TQP 41.555
Pocket No.: 2; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 5k8b.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1E4I NFG 1.73697
2 4XJ7 ADN 1.87266
3 2F5X ASP 1.92308
4 5AYI BGC 1.98511
5 5UZ8 GSH 2.48139
6 6C3C EJ1 3.22581
7 2F7A CCU 3.22581
8 5MB4 NAG 3.49127
9 4GNC ASO 3.67893
10 1QH9 LAC 3.87931
11 2G3F IZC 3.97022
12 5OSW DIU 3.97022
13 2HPL ASP ASP LEU TYR GLY 4
14 6C9B EGV 4.52128
15 4XDZ 40E 4.95627
16 4P83 U5P 5.49451
17 6EK3 OUL 6.33484
18 5U75 SIA GAL NDG FUC 7.14286
19 1I7Q PYR 8.29016
20 5EB4 FAD 8.68486
21 4B1M FRU FRU 12.4324
22 4QAG F95 12.782
23 5H3A UMP 13.0742
24 1XVB BHL 14.7059
25 4C1K PEP 23.2824
26 1O4T OXL 24.0602
Pocket No.: 3; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5k8b.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1A5V Y3 1.26582
2 2GVV DI9 2.2293
3 1F0X FAD 2.23325
4 1QFT HSM 2.28571
5 3OZ2 FAD 2.51889
6 4XZ3 ACP 3.04348
7 5E4R 40E 4.21836
8 6F5U CQN 5.15152
Pocket No.: 4; Query (leader) PDB : 5K8B; Ligand: PDG; Similar sites found with APoc: 14
This union binding pocket(no: 4) in the query (biounit: 5k8b.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6HKE LMR 1.88679
2 5TDC NMM ILE PHE SER 2.63158
3 2P7Q GG6 3.00752
4 1ONX ASP 3.07692
5 4I9A NCN 3.47222
6 2GRU EXO 3.72208
7 4JCA CIT 4.19162
8 3LJU IP9 4.40415
9 5N18 8HZ 6.42202
10 5T7I LAT NAG GAL 6.45161
11 3M0J OAF 6.51466
12 5AYE BMA BMA 9.55224
13 2IMP LAC 13.8958
14 6MJ7 ARG 16.3636
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