Receptor
PDB id Resolution Class Description Source Keywords
3EI5 2.05 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FRO ARABIDOPSIS THALIANA COMPLEXED WITH PLP-GLU: AN EXTERNAL ALM IMIC 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:436;
B:434;
B:436;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
PGU A:433;
B:433;
 Valid;
Valid;
 none;
none;
 submit data
378.272 C13 H19 N2 O9 P Cc1c(...
SO4 A:435;
B:435;
 Invalid;
Invalid;
 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: PGU; Similar ligands found: 68
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 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 0PR 0.688312 0.920635
17 PDA 0.685714 0.888889
18 PP3 0.685714 0.888889
19 PDD 0.685714 0.888889
20 2BK 0.666667 0.888889
21 TLP 0.666667 0.888889
22 2BO 0.666667 0.888889
23 AQ3 0.658537 0.878788
24 ILP 0.653333 0.890625
25 EA5 0.649351 0.953125
26 IN5 0.619718 0.857143
27 PLG 0.619718 0.935484
28 KAM 0.609756 0.921875
29 IK2 0.608108 0.892308
30 CBA 0.589744 0.848485
31 PPE 0.589744 0.983871
32 PLA 0.584416 0.907692
33 PMG 0.582278 0.938462
34 P1T 0.573333 0.892308
35 5PA 0.558442 0.921875
36 33P 0.545455 0.84375
37 PSZ 0.53012 0.785714
38 PXP 0.529412 0.774194
39 HEY 0.518072 0.9375
40 3LM 0.511905 0.826087
41 PMH 0.5 0.688312
42 PMP 0.5 0.83871
43 DN9 0.494382 0.884058
44 RW2 0.494253 0.865672
45 PXG 0.494253 0.846154
46 7TS 0.493976 0.696203
47 GT1 0.492958 0.69697
48 DCS 0.488095 0.75
49 PL2 0.488095 0.823529
50 PL6 0.481928 0.825397
51 CKT 0.469136 0.859375
52 9YM 0.454545 0.820895
53 PL8 0.43956 0.819444
54 CAN PLP 0.433333 0.893939
55 1D0 0.431579 0.838235
56 7B9 0.430108 0.855072
57 PLR 0.428571 0.68254
58 PPG 0.423913 0.892308
59 PLP 2KZ 0.423529 0.815385
60 F0G 0.421687 0.75
61 KOU 0.416667 0.8125
62 0JO 0.409639 0.731343
63 Z98 0.409091 0.846154
64 RMT 0.404255 0.779412
65 OJQ 0.402299 0.670886
66 PUS 0.402174 0.702703
67 FEV 0.4 0.705882
68 P0P 0.4 0.725806
Similar Ligands (3D)
Ligand no: 1; Ligand: PGU; Similar ligands found: 25
No: Ligand Similarity coefficient
1 KET 0.9733
2 3QP 0.9723
3 PLP 0A0 0.9657
4 LEU PLP 0.9341
5 SEP PLP 0.9241
6 ASP PLP 0.9238
7 GLU PLP 0.9237
8 PLP 2ML 0.9213
9 PLP PHE 0.9183
10 PM9 0.9073
11 MET PLP 0.9073
12 PLP MET 0.9073
13 P71 0.9004
14 FEJ 0.8965
15 TYR PLP 0.8941
16 GAB PLP 0.8828
17 PLP CYS 0.8815
18 GBC PLP 0.8800
19 SER PLP 0.8744
20 6DF 0.8720
21 PLP SER 0.8719
22 PLP BH2 0.8707
23 PL5 0.8672
24 HCP 0.8622
25 EVM 0.8568
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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