Receptor
PDB id Resolution Class Description Source Keywords
3EI9 1.55 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF K270N VARIANT OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH LE XTERNAL ALDIMINE FORM ARABIDOPSIS THALIANA AMINOTRANSFERASE LYSINE BIOSYNTHESIS PYRIDOXAL 5-prime PHOSPHATEXTERNAL ALDIMINE LL-DIAMINOPIMELATE CHLOROPLAST PYRIDOXPHOSPHATE TRANSFERASE TRANSIT PEPTIDE
Ref.: MECHANISM OF SUBSTRATE RECOGNITION AND PLP-INDUCED CONFORMATIONAL CHANGES IN LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA. J.MOL.BIOL. V. 384 1314 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:434;
A:435;
A:436;
B:434;
B:435;
B:436;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PL6 A:433;
B:433;
Valid;
Valid;
none;
none;
submit data
376.256 C13 H17 N2 O9 P Cc1c(...
SO4 A:437;
A:438;
B:437;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EI9 1.55 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF K270N VARIANT OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH LE XTERNAL ALDIMINE FORM ARABIDOPSIS THALIANA AMINOTRANSFERASE LYSINE BIOSYNTHESIS PYRIDOXAL 5-prime PHOSPHATEXTERNAL ALDIMINE LL-DIAMINOPIMELATE CHLOROPLAST PYRIDOXPHOSPHATE TRANSFERASE TRANSIT PEPTIDE
Ref.: MECHANISM OF SUBSTRATE RECOGNITION AND PLP-INDUCED CONFORMATIONAL CHANGES IN LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA. J.MOL.BIOL. V. 384 1314 2008
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
2 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
4 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
5 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
7 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
8 3EIA - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FL0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
3 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
5 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
6 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
7 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
8 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
9 3EIA - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FL0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 2Z1Z - MLT C4 H6 O5 C([C@H](C(....
3 3EIB - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 3EI8 - PL5 C15 H22 N3 O9 P Cc1c(c(c(c....
5 3EI6 - PL4 C15 H24 N3 O9 P Cc1c(c(c(c....
6 2Z20 - PLP C8 H10 N O6 P Cc1c(c(c(c....
7 3EI9 - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
8 3EI5 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
9 3EIA - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PL6; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 PL6 1 1
2 KOU 0.761194 0.87931
3 PL5 0.706667 0.913793
4 5DK 0.679487 0.854839
5 PUS 0.662338 0.776119
6 EPC 0.637681 0.872727
7 0JO 0.611111 0.87931
8 PLT 0.604651 0.836066
9 Z98 0.597403 0.883333
10 4LM 0.589041 0.862069
11 6DF 0.564103 0.824561
12 LLP 0.560976 0.868852
13 EXT 0.540541 0.910714
14 PLP 0.522388 0.818182
15 MPM 0.519481 0.859649
16 PLP PHE 0.517241 0.810345
17 PZP 0.514706 0.821429
18 AN7 0.506667 0.821429
19 HCP 0.506329 0.847458
20 P3D 0.506329 0.806452
21 FOO 0.5 0.859649
22 P89 0.494253 0.784615
23 3QP 0.493671 0.888889
24 PDG 0.481928 0.825397
25 PGU 0.481928 0.825397
26 PFM 0.481928 0.847458
27 PLP PVH 0.478261 0.731343
28 KET 0.46988 0.929825
29 PLP ABU 0.464286 0.844828
30 76U 0.453488 0.8125
31 O1G 0.450549 0.793651
32 N5F 0.448276 0.8125
33 EA5 0.448276 0.787879
34 PLP PUT 0.440476 0.762712
35 PLS 0.433735 0.793651
36 PPD 0.428571 0.822581
37 PDD 0.426829 0.75
38 PP3 0.426829 0.75
39 PDA 0.426829 0.75
40 PLP MYB 0.425532 0.710145
41 QLP 0.425287 0.776119
42 PLG 0.425 0.793651
43 P0P 0.424658 0.785714
44 PY5 0.423529 0.772727
45 2BO 0.416667 0.75
46 TLP 0.416667 0.75
47 2BK 0.416667 0.75
48 PLR 0.414286 0.767857
49 7XF 0.413793 0.796875
50 C6P 0.411765 0.793651
51 PXP 0.410959 0.716667
52 KAM 0.408602 0.784615
53 AQ3 0.40625 0.746269
54 PY6 0.404494 0.75
55 PLP 142 0.4 0.757576
56 ORX 0.4 0.784615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DR4 G4M 0.003487 0.42573 1.79028
2 5W70 9YM 0.001624 0.41007 1.85185
3 5GVL GI8 0.00937 0.40817 1.85185
4 5GVL PLG 0.00937 0.40817 1.85185
5 5W71 9YM 0.00789 0.4124 2.27273
6 5W71 PLP 0.0009345 0.41074 2.27273
7 2FNU PMP UD1 0.009083 0.40568 2.93333
8 2TPL HPP 0.002207 0.4185 3.24074
9 2WK9 PLG 0.004199 0.41534 3.59897
10 2WK9 PLP 0.004384 0.41197 3.59897
11 4ZAH T5K 0.004942 0.40705 3.93519
12 3B8X G4M 0.005708 0.41209 4.10256
13 1FC4 AKB PLP 0.001068 0.40877 4.2394
14 1O69 X04 0.01284 0.40925 4.31472
15 4JE5 PMP 0.000000004328 0.55534 4.39815
16 4JE5 PLP 0.000000005773 0.55154 4.39815
17 2PO3 T4K 0.004401 0.4169 4.39815
18 3ZRR PXG 0.001075 0.4175 4.6875
19 3FRK TQP 0.002136 0.4264 4.86111
20 1DJ9 KAM 0.0006577 0.4107 4.94792
21 4IY7 0JO 0.001915 0.40926 5.54156
22 4IY7 KOU 0.002031 0.40834 5.54156
23 4IYO 0JO 0.001915 0.40534 5.54156
24 1E5F PLP 0.0006999 0.41293 5.94059
25 5X30 7XF 0.0002637 0.43458 6.03015
26 5X2Z 3LM 0.001044 0.43184 6.03015
27 5X30 4LM 0.0008323 0.41282 6.03015
28 2X5F PLP 0.00000004503 0.53348 7.2093
29 2XBN PMP 0.002923 0.41349 7.49415
30 4AZJ SEP PLP 0.001089 0.4196 7.77778
31 2CST MAE 0.0001787 0.40116 8.0292
32 5IWQ PLP 0.000001309 0.49466 8.10185
33 2OGA PGU 0.0007381 0.42622 8.5213
34 2FYF PLP 0.000154 0.40512 8.54271
35 5U23 TQP 0.002504 0.4235 8.56481
36 2HOX P1T 0.0000000002685 0.65683 8.66511
37 2R5E QLP 0.000000001119 0.64396 8.85781
38 2R5C C6P 0.000000001191 0.6427 8.85781
39 4RKC PMP 0.0000004728 0.51963 10.3015
40 1TOI HCI 0.00004242 0.53108 10.4167
41 3PDB PMP 0.0000001234 0.528 10.9726
42 3PD6 PMP 0.00000009363 0.52262 10.9726
43 1YAA MAE 0.00005314 0.41933 11.165
44 1LC8 33P 0.0000001687 0.58969 11.2637
45 2AY3 MPP 0.0001844 0.42864 12.9442
46 5DJ3 5DK 0.00000849 0.4918 14.3617
47 1GEX PLP HSA 0.00000006028 0.60558 14.5833
48 1OXO IK2 0.000002739 0.5668 15.0463
49 4R5Z PMP 0.00000004262 0.599 16.8937
50 4R5Z SIN 0.000000149 0.59426 16.8937
51 2R2N PMP 0.00000003228 0.67831 17.6471
52 2R2N KYN 0.001947 0.47142 17.6471
53 3BWN PMP PHE 0.000000002477 0.63923 19.6759
54 3BWN PMP 0.00000001387 0.55651 19.6759
55 1UU1 PMP HSA 0.00000001304 0.61047 19.7015
56 5T4J PLP ABU 0.003197 0.42399 20.5479
57 3FVU IAC 0.000005409 0.42435 22.7488
58 4M2K PLP 0.0000001604 0.49733 22.9064
59 1C7O PPG 0.0000001496 0.5611 22.9167
60 3E2Y PMP 0.00000001231 0.55066 23.6585
61 1M7Y PPG 0.00000002252 0.63301 24.0741
62 3CQ5 PMP 0.000000002558 0.53296 28.7263
63 1AJS PLA 0.00000004684 0.60469 29.1667
64 2ZYJ PGU 0.00000000137 0.67581 31.4815
65 3B1E P1T 0.00000000484 0.57792 34.0278
66 1V2F HCI 0.000006483 0.44948 34.3832
67 1U08 PLP 0.00000001627 0.54085 36.0104
68 1GCK ASP PLP 0.000000009825 0.60881 36.3426
69 2ZC0 PMP 0.00000001193 0.58309 38.8889
70 2X5D PLP 0.0000000004822 0.5367 39.5631
71 1GDE GLU PLP 0.000000002851 0.61871 40.1028
72 1XI9 PLP 0.00000004853 0.5132 41.6256
Pocket No.: 2; Query (leader) PDB : 3EI9; Ligand: PL6; 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: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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