Receptor
PDB id Resolution Class Description Source Keywords
2OGA 2.05 Å EC: 2.-.-.- X-RAY CRYSTAL STRUCTURE OF S. VENEZUELAE DESV IN COMPLEX WITH KETIMINE INTERMEDIATE STREPTOMYCES VENEZUELAE PLP-DEPENDENT ENZYME DESOSAMINE TRANSAMINASE DEOXYSUGARSANTIBIOTICS HYDROLASE
Ref.: MOLECULAR ARCHITECTURE OF DESV FROM STREPTOMYCES VENEZUELAE: A PLP-DEPENDENT TRANSAMINASE INVOLVED IN THE BIOSYNTHESIS OF THE UNUSUAL SUGAR DESOSAMINE. PROTEIN SCI. V. 16 887 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:380;
B:380;
C:380;
D:380;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
EDO A:1023;
A:1024;
B:381;
B:382;
C:1026;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NA A:1022;
C:1025;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
PGU A:1020;
B:1021;
C:1023;
D:1024;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
378.272 C13 H19 N2 O9 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OGA 2.05 Å EC: 2.-.-.- X-RAY CRYSTAL STRUCTURE OF S. VENEZUELAE DESV IN COMPLEX WITH KETIMINE INTERMEDIATE STREPTOMYCES VENEZUELAE PLP-DEPENDENT ENZYME DESOSAMINE TRANSAMINASE DEOXYSUGARSANTIBIOTICS HYDROLASE
Ref.: MOLECULAR ARCHITECTURE OF DESV FROM STREPTOMYCES VENEZUELAE: A PLP-DEPENDENT TRANSAMINASE INVOLVED IN THE BIOSYNTHESIS OF THE UNUSUAL SUGAR DESOSAMINE. PROTEIN SCI. V. 16 887 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 2OGA - PGU 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 211 families.
1 2OGA - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 5U21 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
2 5U23 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
3 5U24 - 7SG C24 H35 N4 O19 P3 Cc1c(c(c(c....
4 1O61 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 3FRK - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
6 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
7 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(c....
8 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
9 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
10 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
11 1MDZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
12 2OGA - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGU; 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 : 2OGA; Ligand: PGU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2oga.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: 98
This union binding pocket(no: 2) in the query (biounit: 2oga.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3FQ8 PMP 0.002937 0.41666 1.25313
2 2C5S AMP 0.01752 0.40755 1.50376
3 5DJ3 5DK 0.002284 0.42497 1.59574
4 5BU2 AMP 0.002107 0.47569 1.75439
5 2JBH 5GP 0.009639 0.4206 1.77778
6 3B1E P1T 0.01119 0.40519 1.78571
7 1JG0 UMP 0.02624 0.4037 1.89394
8 3IP5 ALA 0.02928 0.40135 1.96629
9 4FL0 PLP 0.0004432 0.47576 2.00501
10 1FC4 AKB PLP 0.001063 0.43942 2.25564
11 1PMO PLR 0.002764 0.43795 2.25564
12 1AJS PLA 0.0006632 0.42871 2.50627
13 3BS8 PMP 0.008909 0.41373 2.50627
14 5G4J EXT 0.004176 0.41357 2.50627
15 1W6F ISZ 0.02803 0.40058 2.51799
16 4B98 PXG 0.008719 0.403 2.75689
17 1VJO PLP 0.001113 0.44717 2.79898
18 5IWQ PLP 0.003576 0.43263 3.00752
19 4ZSY RW2 0.005947 0.40033 3.00752
20 3WCS MAN NAG GAL 0.01102 0.41336 3.14961
21 3WCS MAN NAG 0.01955 0.40943 3.14961
22 1LC8 33P 0.0006838 0.41098 3.2967
23 1U08 PLP 0.0007041 0.47165 3.36788
24 3G2Y GF4 0.03074 0.40455 3.42205
25 1E5F PLP 0.0006304 0.45837 3.50877
26 1DFO PLG 0.002651 0.41055 3.50877
27 1M32 PLP 0.01103 0.42226 3.55191
28 2Z9V PXM 0.0009544 0.47689 3.57143
29 1GEX PLP HSA 0.001395 0.40628 3.93258
30 4RKC PMP 0.001064 0.45272 4.0201
31 2FYF PLP 0.005783 0.43173 4.0201
32 3CQ5 PMP 0.002553 0.45496 4.51128
33 4JYM KKN 0.03502 0.40235 4.81482
34 3PD6 PMP 0.0002829 0.49094 5.01253
35 3PDB PMP 0.0002409 0.48834 5.01253
36 4UOX PLP 0.00296 0.43653 5.01253
37 4KTP BGC 0.01022 0.42505 5.01253
38 4UOX PUT 0.003569 0.42418 5.01253
39 4UOX PLP PUT 0.006365 0.40909 5.01253
40 4UHO PLP 0.001801 0.46273 5.12821
41 4ADC PLP 0.002237 0.44233 5.26316
42 5DDW 5B6 0.003708 0.40891 5.26316
43 4WXG 2BO 0.002189 0.40749 5.26316
44 1JS3 PLP 142 0.008125 0.40098 5.26316
45 4LNL PLG 0.0007032 0.46108 5.40541
46 4LNL 2BO 0.001347 0.44341 5.40541
47 1DJ9 KAM 0.001901 0.43661 5.72917
48 1Z17 ILE 0.014 0.41894 5.81395
49 2GMP NAG MAN 0.02292 0.40766 5.95238
50 1ICV NIO 0.02093 0.4018 5.99078
51 1PIG GLC GLC 0.02745 0.40279 6.01504
52 1ELU PDA 0.002275 0.42505 6.15385
53 1ELU CSS 0.0037 0.40894 6.15385
54 4BA5 PXG 0.001944 0.43616 7.01754
55 1ZC9 PMP 0.001373 0.43458 7.01754
56 2OAT PFM 0.004574 0.41547 7.01754
57 1IK4 PGH 0.01388 0.40453 7.23684
58 4UCI ADN 0.01019 0.43297 7.5188
59 1S14 NOV 0.01767 0.41171 7.73196
60 4JE5 PMP 0.004352 0.43309 7.76942
61 4JE5 PLP 0.004405 0.43283 7.76942
62 1W62 PYC 0.02295 0.40582 7.76942
63 1UU1 PMP HSA 0.004452 0.40559 8.35821
64 3EI9 PL6 0.0007381 0.42622 8.5213
65 1XXR MAN 0.01027 0.42423 8.69565
66 2R2N PMP 0.0007411 0.46514 9.02256
67 2BES RES 0.01313 0.40568 9.30233
68 1SFF IK2 0.005535 0.40487 10.0251
69 2Y7P SAL 0.02939 0.40024 10.0917
70 2X2T GAL NGA 0.0174 0.42371 10.4575
71 4WOH 4NP 0.009889 0.4223 11.4458
72 3K7S R52 0.01144 0.41257 11.7318
73 3E2Y PMP 0.0006837 0.4668 11.7794
74 4IY7 KOU 0.0004132 0.45285 11.8388
75 4IYO 0JO 0.000449 0.45131 11.8388
76 4IY7 0JO 0.0004891 0.44973 11.8388
77 2R5E QLP 0.003547 0.4131 12.0301
78 2R5C C6P 0.00505 0.40656 12.0301
79 2ZC0 PMP 0.000304 0.46777 14.0351
80 3ZRR PXG 0.002777 0.41763 14.5833
81 1GDE GLU PLP 0.002994 0.41986 14.653
82 4R5Z PMP 0.001446 0.42098 14.9864
83 1GCK ASP PLP 0.001954 0.42413 15.5844
84 5X30 4LM 0.001782 0.43367 20.603
85 5X2Z 3LM 0.001452 0.43296 20.603
86 5X30 7XF 0.00193 0.42816 20.603
87 1LW4 TLP 0.001373 0.41667 21.0375
88 1LW4 PLP 0.001193 0.40744 21.0375
89 3WGC PLG 0.0008691 0.45204 21.1144
90 3B8X G4M 0.00000000849 0.52617 27.9487
91 5K8B PDG 0.00000000314 0.64726 35.3383
92 4ZAH T5K 0.00000001118 0.56919 38.8889
93 2PO3 T4K 0.00000006 0.50177 39.3484
94 5W70 9YM 0.00000002498 0.6323 40.1003
95 5W71 9YM 0.00000002039 0.66976 42.3559
96 5W71 PLP 0.0000000002602 0.66972 42.3559
97 1B9I PXG 0.0000001462 0.56827 43.8144
98 4K2M O1G 0.0000000006133 0.67543 49.6241
Pocket No.: 3; Query (leader) PDB : 2OGA; Ligand: PGU; 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: 2oga.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2oga.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2oga.bio3) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2oga.bio3) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2oga.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2OGA; Ligand: PGU; Similar sites found: 7
This union binding pocket(no: 8) in the query (biounit: 2oga.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ISK UMP 0.02283 0.40176 1.89394
2 1WYV PLP AOA 0.00963 0.40456 2.25564
3 3TUR 6CL 0.02138 0.40904 2.43902
4 5KTQ DCP 0.02131 0.40027 5.51378
5 5EOO CIT 0.004268 0.44834 6.03774
6 4RJD TFP 0.02785 0.40146 6.06061
7 2P1E LAC 0.01719 0.41249 6.75241
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