Receptor
PDB id Resolution Class Description Source Keywords
4UOX 2.08 Å EC: 2.6.1.82 CRYSTAL STRUCTURE OF YGJG IN COMPLEX WITH PYRIDOXAL-5'-PHOSP AND PUTRESCINE ESCHERICHIA COLI TRANSFERASE POLYAMINE
Ref.: STRUCTURE OF PUTRESCINE AMINOTRANSFERASE FROM ESCHE COLI PROVIDES INSIGHTS INTO THE SUBSTRATE SPECIFICI CLASS III AMINOTRANSFERASES. PLOS ONE V. 9 13212 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMT C:1460;
C:1459;
D:1462;
A:1460;
A:1461;
D:1460;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
GOL D:1461;
B:1460;
A:1462;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PLP C:800;
D:800;
Valid;
Valid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
PLP PUT A:800;
B:800;
Valid;
Valid;
none;
none;
submit data
316.274 n/a [P+](...
PEG C:1461;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
PUT C:801;
Valid;
none;
submit data
88.151 C4 H12 N2 C(CCN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UOX 2.08 Å EC: 2.6.1.82 CRYSTAL STRUCTURE OF YGJG IN COMPLEX WITH PYRIDOXAL-5'-PHOSP AND PUTRESCINE ESCHERICHIA COLI TRANSFERASE POLYAMINE
Ref.: STRUCTURE OF PUTRESCINE AMINOTRANSFERASE FROM ESCHE COLI PROVIDES INSIGHTS INTO THE SUBSTRATE SPECIFICI CLASS III AMINOTRANSFERASES. PLOS ONE V. 9 13212 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4UOX - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4UOY - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4UOX - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4UOY - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4UOX - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4UOY - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Ligand no: 2; Ligand: PLP PUT; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP PUT 1 1
2 PLP ABU 0.742857 0.907407
3 P3D 0.638889 0.830508
4 LLP 0.5875 0.803279
5 EXT 0.569444 0.839286
6 Z98 0.525 0.758065
7 0JO 0.513158 0.721311
8 PLP MYB 0.494382 0.753846
9 4LM 0.493506 0.704918
10 EPC 0.493333 0.767857
11 PLP PHE 0.488636 0.836364
12 PLP PVH 0.467391 0.69697
13 P89 0.465909 0.75
14 PLP 0.463768 0.684211
15 PLP 142 0.463158 0.69697
16 KOU 0.4625 0.75
17 6DF 0.457831 0.754386
18 PZP 0.457143 0.75
19 MPM 0.45 0.758621
20 PL5 0.443182 0.754098
21 PL6 0.440476 0.762712
22 HCP 0.439024 0.810345
23 5DK 0.428571 0.761905
24 PLP PMP 0.4125 0.75
25 FOO 0.4125 0.7
26 PUS 0.411111 0.642857
27 AN7 0.4 0.661017
Ligand no: 3; Ligand: PUT; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PUT 1 1
2 13D 0.666667 0.8
3 16D 0.636364 0.9
4 N2P 0.636364 0.947368
5 DIA 0.583333 0.9
6 AML 0.5 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UOX; Ligand: PLP; 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: 4uox.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4UOX; Ligand: PLP; Similar sites found: 94
This union binding pocket(no: 2) in the query (biounit: 4uox.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5GVL GI8 0.01479 0.42436 1.58371
2 5GVL PLG 0.01479 0.42436 1.58371
3 3VP6 HLD 0.0004621 0.48064 1.71306
4 5X2Z 3LM 0.00222 0.44938 1.75879
5 5X30 4LM 0.001949 0.40904 1.75879
6 5X30 7XF 0.001543 0.4064 1.75879
7 1PMO PLR 0.002397 0.42796 1.93133
8 4AZJ SEP PLP 0.003986 0.43038 2.22222
9 4K2M O1G 0.0001014 0.50836 2.25734
10 5JXZ ISC 0.01155 0.40291 2.30179
11 1AJS PLA 0.0131 0.40895 2.42718
12 2R5C C6P 0.008838 0.41214 2.7972
13 2R5E QLP 0.009349 0.41098 2.7972
14 1LW4 TLP 0.00007825 0.50688 2.88184
15 1LW4 PLP 0.00006064 0.50688 2.88184
16 4BNU 9KQ 0.00441 0.43005 2.97398
17 1I0Z NAI 0.02072 0.40734 3.003
18 2FYF PLP 0.0008578 0.4385 3.01508
19 3ZRR PXG 0.00008835 0.50678 3.125
20 3E2Y PMP 0.006431 0.4083 3.17073
21 1K1Y MAL 0.02096 0.40255 3.21199
22 1YZN GNP 0.02128 0.40161 3.24324
23 1VG8 GNP 0.01667 0.40679 3.38164
24 5K8B PDG 0.00009276 0.51021 3.47395
25 2YG3 FAD 0.02823 0.41087 3.53201
26 5I0H ADP BEF 0.01377 0.40299 3.64026
27 4CMF PXG 0.01357 0.4082 3.72671
28 2Z9V PXM 0.0003753 0.44596 3.82653
29 5W71 PLP 0.0001362 0.49313 3.86364
30 5W71 9YM 0.000704 0.4927 3.86364
31 5SZH GNP 0.02179 0.40111 3.92157
32 1E5F PLP 0.002394 0.43275 3.9604
33 5W70 9YM 0.0003474 0.47867 4.04494
34 4YNU LGC 0.03379 0.41328 4.06852
35 4YNU FAD 0.02951 0.41328 4.06852
36 4Q3F TLA 0.005136 0.40635 4.2735
37 1JS3 PLP 142 0.008828 0.41033 4.28266
38 3WXM GTP 0.01839 0.40181 4.28266
39 3FRK TQP 0.0006291 0.48376 4.28954
40 4ZG4 VO4 ADP 0.01479 0.40484 4.49679
41 4CE5 PDG 0.01436 0.40996 4.5045
42 1DFO PLG 0.001256 0.45227 4.55635
43 1MDZ DCS 0.02183 0.40965 4.83461
44 1MDZ PLP 0.02075 0.40965 4.83461
45 3B8X G4M 0.000231 0.50962 4.87179
46 2OGA PGU 0.00296 0.43653 5.01253
47 2FNU PMP UD1 0.002914 0.45697 5.06667
48 2WK9 PLG 0.0007143 0.48244 5.14139
49 2WK9 PLP 0.001619 0.46207 5.14139
50 1M32 PLP 0.0006666 0.42986 5.46448
51 4Q4K FMN 0.01014 0.41732 5.60224
52 5MDH NAD 0.02303 0.40258 5.70571
53 4LNL 2BO 0.0004005 0.46882 6.60661
54 4LNL PLG 0.0003811 0.46726 6.60661
55 1OIV GDP 0.01356 0.40972 7.32984
56 1OIX GDP 0.0214 0.40009 7.32984
57 1U08 PLP 0.001991 0.42632 7.51295
58 2D7C GTP 0.01883 0.4028 7.78443
59 2HV8 GTP 0.01572 0.40661 8.13953
60 1WYV PLP AOA 0.003391 0.42787 9.07173
61 3PD6 PMP 0.001025 0.43881 9.22693
62 3PDB PMP 0.001672 0.43513 9.22693
63 3TKL GTP 0.006549 0.42346 11.2245
64 5U23 TQP 0.001007 0.47366 12.0419
65 5UQW GDP 0.01952 0.40056 13.7566
66 1B9I PXG 0.0005433 0.47543 14.9485
67 2C5L GTP 0.01396 0.41057 15.0289
68 1VJO PLP 0.001321 0.44475 16.285
69 3WGC PLG 0.0001515 0.48842 17.5953
70 1DJ9 KAM 0.001747 0.41778 21.3542
71 1FC4 AKB PLP 0.01101 0.4058 23.9401
72 1TU3 GNP 0.02107 0.40182 25.3165
73 5DDW 5B6 0.00000000005151 0.65119 30.621
74 4AOA IK2 0.0000000005402 0.74134 31.7181
75 4UHO PLP 0.000000003358 0.73345 33.1906
76 3FQ8 PMP 0.00000000008026 0.80333 33.7237
77 4B98 PXG 0.000000000871 0.7358 33.9286
78 2CJH AKG 0.000000002085 0.71411 34.5212
79 3A8U PLP 0.000000002902 0.62622 34.5212
80 4ZM4 PLP 0.0000000001923 0.72958 35.123
81 4ZM4 P3B 0.000000003881 0.60645 35.123
82 5KGS 6SR 0.000000002406 0.77615 35.2298
83 4E3Q PMP 0.0000000003196 0.72515 35.3319
84 3BS8 PMP 0.000000003273 0.6965 35.8447
85 4ZSY RW2 0.0000000002129 0.63034 36.4425
86 4BA5 PXG 0.000000002264 0.66165 39.6514
87 1SFF IK2 0.0000000000003112 0.90635 41.784
88 5G09 6DF 0.00000000003882 0.80727 43.469
89 5G4J EXT 0.000000002532 0.62511 44.3946
90 5WYF ILP 0.00000000009258 0.78943 45.0216
91 1ZC9 PMP 0.00000001547 0.68097 45.7275
92 1MLY ACZ PLP 0.000000003307 0.71247 45.9207
93 2OAT PFM 0.000000000185 0.68786 47.1526
94 4ADC PLP 0.000000000002379 0.66035 48.5222
Pocket No.: 3; Query (leader) PDB : 4UOX; Ligand: PLP PUT; Similar sites found: 49
This union binding pocket(no: 3) in the query (biounit: 4uox.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VP6 HLD 0.001399 0.44374 1.71306
2 1PMO PLR 0.001986 0.40904 1.93133
3 4AZJ SEP PLP 0.002594 0.42643 2.22222
4 4K2M O1G 0.001848 0.43482 2.25734
5 1LW4 TLP 0.00118 0.43757 2.88184
6 1LW4 PLP 0.000864 0.43543 2.88184
7 4BNU 9KQ 0.009859 0.40229 2.97398
8 2FYF PLP 0.001637 0.40609 3.01508
9 3ZRR PXG 0.001053 0.44183 3.125
10 5K8B PDG 0.005286 0.41441 3.47395
11 5W71 9YM 0.0132 0.41722 3.86364
12 5W71 PLP 0.004195 0.41136 3.86364
13 5W70 9YM 0.008832 0.40099 4.04494
14 1JS3 PLP 142 0.007745 0.40167 4.28266
15 3FRK TQP 0.007942 0.41794 4.28954
16 1DFO PLG 0.006408 0.40716 4.55635
17 3B8X G4M 0.003615 0.43754 4.87179
18 2OGA PGU 0.006365 0.40909 5.01253
19 2WK9 PLP 0.006274 0.42141 5.14139
20 2WK9 PLG 0.007877 0.41933 5.14139
21 1M32 PLP 0.001281 0.40043 5.46448
22 4LO2 GAL BGC 0.02186 0.40721 7.48299
23 1IIM TTP 0.01782 0.40808 10.9589
24 5U23 TQP 0.01674 0.40286 12.0419
25 3KIV ACA 0.02271 0.4006 15.1899
26 1VJO PLP 0.00214 0.41931 16.285
27 3WGC PLG 0.002457 0.41671 17.5953
28 5DDW 5B6 0.0000000001177 0.68332 30.621
29 4AOA IK2 0.000000003236 0.66597 31.7181
30 4UHO PLP 0.000000008863 0.7246 33.1906
31 3FQ8 PMP 0.000000001437 0.71067 33.7237
32 4B98 PXG 0.000000007503 0.66186 33.9286
33 2CJH AKG 0.00000003925 0.61805 34.5212
34 3A8U PLP 0.000000008481 0.55977 34.5212
35 4ZM4 PLP 0.00000001716 0.66508 35.123
36 4ZM4 P3B 0.000000008007 0.63048 35.123
37 5KGS 6SR 0.00000003777 0.6868 35.2298
38 4E3Q PMP 0.000000001675 0.63529 35.3319
39 3BS8 PMP 0.00000006629 0.58537 35.8447
40 4ZSY RW2 0.000000002528 0.63232 36.4425
41 4BA5 PXG 0.0000001575 0.61248 39.6514
42 1SFF IK2 0.00000000001503 0.78801 41.784
43 5G09 6DF 0.000000001744 0.69692 43.469
44 5G4J EXT 0.00000008865 0.60053 44.3946
45 5WYF ILP 0.0000000003168 0.7296 45.0216
46 1ZC9 PMP 0.0000005944 0.58221 45.7275
47 1MLY ACZ PLP 0.000000007616 0.66521 45.9207
48 2OAT PFM 0.0000000004406 0.71551 47.1526
49 4ADC PLP 0.00000000003607 0.66942 48.5222
Pocket No.: 4; Query (leader) PDB : 4UOX; Ligand: PUT; Similar sites found: 93
This union binding pocket(no: 4) in the query (biounit: 4uox.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5GVL GI8 0.03102 0.40141 1.58371
2 5GVL PLG 0.03102 0.40141 1.58371
3 3VP6 HLD 0.000533 0.46739 1.71306
4 5DJ3 5DK 0.007738 0.40526 1.8617
5 1PMO PLR 0.0021 0.41521 1.93133
6 3ZFD ANP 0.004539 0.40689 2.14133
7 4AZJ SEP PLP 0.002206 0.43367 2.22222
8 4K2M O1G 0.0008436 0.45456 2.25734
9 4TMZ GSP 0.013 0.40025 2.6087
10 1LW4 TLP 0.0006105 0.4548 2.88184
11 1LW4 PLP 0.0005047 0.45384 2.88184
12 3C3N FMN 0.02674 0.40071 2.88462
13 4BNU 9KQ 0.01076 0.40402 2.97398
14 2FYF PLP 0.001384 0.41569 3.01508
15 3ZRR PXG 0.0007585 0.45269 3.125
16 1YZN GNP 0.007424 0.41611 3.24324
17 1VG8 GNP 0.0123 0.40591 3.38164
18 4LHW GNP 0.0123 0.40444 3.44828
19 3TNF GNP 0.01704 0.40068 3.44828
20 5K8B PDG 0.001954 0.43791 3.47395
21 2Z9V PXM 0.001003 0.41357 3.82653
22 4RD0 GDP 0.007023 0.41081 3.85542
23 5W71 9YM 0.007533 0.43249 3.86364
24 5W71 PLP 0.002348 0.42646 3.86364
25 5SZH GNP 0.01335 0.40425 3.92157
26 5W70 9YM 0.004445 0.41801 4.04494
27 1JS3 PLP 142 0.004287 0.4168 4.28266
28 3WXM GTP 0.01127 0.40622 4.28266
29 3FRK TQP 0.00434 0.43395 4.28954
30 4ZG4 VO4 ADP 0.008418 0.40891 4.49679
31 1DFO PLG 0.003042 0.42546 4.55635
32 1MDZ DCS 0.02213 0.40258 4.83461
33 1MDZ PLP 0.02098 0.40258 4.83461
34 3B8X G4M 0.002304 0.45081 4.87179
35 2OGA PGU 0.003569 0.42418 5.01253
36 2FNU PMP UD1 0.02145 0.40638 5.06667
37 2WK9 PLG 0.004038 0.43671 5.14139
38 2WK9 PLP 0.00537 0.42828 5.14139
39 1M32 PLP 0.0008374 0.41255 5.46448
40 1NF3 GNP 0.01078 0.4071 5.46875
41 5UWP GNP 0.01247 0.40705 6.32911
42 5UWI GNP 0.01504 0.40185 6.32911
43 4LNL 2BO 0.004048 0.41377 6.60661
44 4LNL PLG 0.00343 0.41128 6.60661
45 1IBR GNP 0.01304 0.40473 6.94444
46 3GJX GTP 0.01468 0.40234 6.94444
47 1OIX GDP 0.01021 0.40819 7.32984
48 1WA5 GTP 0.01624 0.40553 8.52273
49 4KVG GTP 0.006933 0.41598 8.92857
50 1WYV PLP AOA 0.007736 0.40332 9.07173
51 5WDR GNP 0.01499 0.40191 9.94152
52 3TKL GTP 0.009156 0.40885 11.2245
53 4HDO GNP 0.009367 0.41142 11.3772
54 3WYG GTP 0.01658 0.40125 11.8421
55 5U23 TQP 0.01206 0.41288 12.0419
56 1KMQ GNP 0.01018 0.40512 12.5
57 3NKV GNP 0.00905 0.41063 12.5714
58 1CXZ GSP 0.008953 0.406 12.6374
59 4XOI GTP 0.01171 0.40392 12.7778
60 1B9I PXG 0.006791 0.41482 14.9485
61 2C5L GTP 0.008971 0.41229 15.0289
62 4K81 GTP 0.01433 0.40422 15.2047
63 1NVV GNP 0.009693 0.41073 15.6627
64 2UZI GTP 0.0108 0.40707 15.6627
65 3DDC GNP 0.01421 0.40298 15.6627
66 1VJO PLP 0.0009353 0.44197 16.285
67 3WGC PLG 0.001388 0.43437 17.5953
68 1LFD GNP 0.009322 0.41003 20.6897
69 1DJ9 KAM 0.007982 0.40068 21.3542
70 1FC4 AKB PLP 0.006737 0.40797 23.9401
71 2YKX AKG 0.0001032 0.40893 29.6774
72 5DDW 5B6 0.00000000002721 0.69255 30.621
73 4AOA IK2 0.000000003508 0.68221 31.7181
74 4UHO PLP 0.000000004961 0.73345 33.1906
75 3FQ8 PMP 0.000000001334 0.72242 33.7237
76 4B98 PXG 0.000000002276 0.69449 33.9286
77 2CJH AKG 0.00000002323 0.64585 34.5212
78 3A8U PLP 0.00000000425 0.58385 34.5212
79 4ZM4 PLP 0.000000005383 0.68418 35.123
80 4ZM4 P3B 0.00000000164 0.646 35.123
81 5KGS 6SR 0.00000001071 0.72253 35.2298
82 4E3Q PMP 0.0000000008512 0.66413 35.3319
83 3BS8 PMP 0.00000002824 0.6154 35.8447
84 4ZSY RW2 0.0000000008055 0.63907 36.4425
85 4BA5 PXG 0.0000003389 0.59432 39.6514
86 1SFF IK2 0.00000000001077 0.80677 41.784
87 5G09 6DF 0.0000000005657 0.72915 43.469
88 5G4J EXT 0.0000000265 0.6114 44.3946
89 5WYF ILP 0.00000000008816 0.76558 45.0216
90 1ZC9 PMP 0.0000002278 0.60856 45.7275
91 1MLY ACZ PLP 0.000000001821 0.70262 45.9207
92 2OAT PFM 0.0000000003012 0.70873 47.1526
93 4ADC PLP 0.000000000006225 0.68063 48.5222
Pocket No.: 5; Query (leader) PDB : 4UOX; Ligand: PLP PUT; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 4uox.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SNN 5RP 0.0261 0.40681 5.72687
2 3VV5 SLZ 0.03257 0.40915 8.35118
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