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 (2D)
Ligand no: 1; Ligand: PL6; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 PL6 1 1
2 KOU 0.761194 0.87931
3 PL5 0.706667 0.913793
4 F0G 0.695652 0.909091
5 5DK 0.679487 0.854839
6 EQJ 0.679487 0.854839
7 PUS 0.662338 0.776119
8 P70 0.662338 0.910714
9 FEJ 0.64 0.862069
10 EPC 0.637681 0.872727
11 0JO 0.611111 0.87931
12 PLT 0.604651 0.836066
13 Q0P 0.6 0.866667
14 Z98 0.597403 0.883333
15 FEV 0.594595 0.847458
16 4LM 0.589041 0.862069
17 SER PLP 0.571429 0.827586
18 EVM 0.565789 0.864407
19 6DF 0.564103 0.824561
20 EXT 0.540541 0.910714
21 PLP 0.522388 0.818182
22 MPM 0.519481 0.859649
23 PLP PHE 0.517241 0.810345
24 PZP 0.514706 0.821429
25 AN7 0.506667 0.821429
26 P3D 0.506329 0.806452
27 HCP 0.506329 0.847458
28 PLP ALO 0.506173 0.810345
29 PLP 999 0.5 0.810345
30 FOO 0.5 0.859649
31 P89 0.494253 0.784615
32 3QP 0.493671 0.888889
33 PDG 0.481928 0.825397
34 PGU 0.481928 0.825397
35 PFM 0.481928 0.847458
36 PLP PVH 0.478261 0.731343
37 LUK 0.47191 0.728571
38 LUH 0.47191 0.728571
39 KET 0.46988 0.929825
40 PLP ABU 0.464286 0.844828
41 GLY PLP 0.4625 0.824561
42 76U 0.453488 0.8125
43 O1G 0.450549 0.793651
44 EA5 0.448276 0.787879
45 N5F 0.448276 0.8125
46 PLS 0.433735 0.793651
47 PPD 0.428571 0.822581
48 PDA 0.426829 0.75
49 PDD 0.426829 0.75
50 PP3 0.426829 0.75
51 PLP MYB 0.425532 0.710145
52 QLP 0.425287 0.776119
53 PLG 0.425 0.793651
54 P0P 0.424658 0.785714
55 PY5 0.423529 0.772727
56 PLP PUT 0.423529 0.774194
57 2BK 0.416667 0.75
58 2BO 0.416667 0.75
59 TLP 0.416667 0.75
60 PLR 0.414286 0.767857
61 7XF 0.413793 0.796875
62 C6P 0.411765 0.793651
63 PXP 0.410959 0.716667
64 LPI 0.409091 0.73913
65 KAM 0.408602 0.784615
66 AQ3 0.40625 0.746269
67 PY6 0.404494 0.75
68 0PR 0.402174 0.78125
69 PLP 142 0.4 0.757576
70 ORX 0.4 0.784615
Similar Ligands (3D)
Ligand no: 1; Ligand: PL6; Similar ligands found: 26
No: Ligand Similarity coefficient
1 PPE 0.9664
2 PLP 0A0 0.9565
3 PLA 0.9540
4 PMG 0.9529
5 3LM 0.9456
6 SEP PLP 0.9447
7 CBA 0.9434
8 ASP PLP 0.9351
9 RW2 0.9151
10 RMT 0.9104
11 PXG 0.8966
12 TYR PLP 0.8951
13 LEU PLP 0.8923
14 PLP 2ML 0.8909
15 PPG 0.8893
16 GBC PLP 0.8880
17 GAB PLP 0.8826
18 P71 0.8824
19 PM9 0.8814
20 MET PLP 0.8814
21 5PA 0.8799
22 PL4 0.8775
23 GLU PLP 0.8772
24 P3B 0.8772
25 ILP 0.8733
26 PLP CYS 0.8657
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found with APoc: 16
This union binding pocket(no: 1) in the query (biounit: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4JE5 PMP 4.39815
2 2HOX P1T 8.66511
3 2HOX P1T 8.66511
4 4R5Z PMP 16.8937
5 3BWN PMP 19.6759
6 5VEQ PMP 23.601
7 5VEQ PMP 23.601
8 5VEQ PMP 23.601
9 5VEQ PMP 23.601
10 3B1E 0JO 34.0278
11 3B1E 0JO 34.0278
12 6F77 PLP 37.037
13 2X5D PLP 39.5631
14 6L1O TYR 42.6065
15 6L1O PMP 42.6065
16 6L1O PLP 42.6065
Pocket No.: 2; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 3ei9.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4JE5 PMP 4.39815
2 2HOX P1T 8.66511
3 2HOX P1T 8.66511
4 3BWN PMP 19.6759
5 5VEQ PMP 23.601
6 5VEQ PMP 23.601
7 6F77 PLP 37.037
8 2X5D PLP 39.5631
9 6L1O TYR 42.6065
10 6L1O PMP 42.6065
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