Receptor
PDB id Resolution Class Description Source Keywords
3EI6 1.9 Å EC: 2.6.1.83 CRYSTAL STRUCTURE OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FRO ARABIDOPSIS THALIANA COMPLEXED WITH PLP-DAP: 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:435;
A:436;
B:435;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
PL4 A:434;
B:433;
 Valid;
Valid;
 none;
none;
 submit data
421.34 C15 H24 N3 O9 P Cc1c(...
SO4 A:433;
B:434;
B:436;
 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: PL4; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 PL4 1 1
2 ORX 0.797297 1
3 PE1 0.786667 1
4 PY6 0.783784 0.924242
5 N5F 0.773333 0.968254
6 PY5 0.753425 0.923077
7 QLP 0.746667 0.924242
8 PGU 0.733333 0.952381
9 PDG 0.733333 0.952381
10 7XF 0.733333 0.952381
11 PLS 0.726027 0.920635
12 LPI 0.723684 0.882353
13 PPD 0.693333 0.920635
14 C6P 0.693333 0.920635
15 PDD 0.631579 0.875
16 PP3 0.631579 0.875
17 PDA 0.631579 0.875
18 ILP 0.625 0.876923
19 0PR 0.619048 0.90625
20 2BO 0.615385 0.875
21 2BK 0.615385 0.875
22 TLP 0.615385 0.875
23 AQ3 0.595506 0.865672
24 IN5 0.571429 0.84375
25 76U 0.571429 0.907692
26 EA5 0.564706 0.938462
27 PLG 0.551282 0.890625
28 KAM 0.550562 0.907692
29 P1T 0.55 0.878788
30 CBA 0.547619 0.835821
31 IK2 0.52439 0.850746
32 PLA 0.52381 0.865672
33 5PA 0.518072 0.907692
34 PL5 0.516854 0.859375
35 33P 0.506024 0.80303
36 PMG 0.505747 0.895522
37 HEY 0.5 0.893939
38 3LM 0.494382 0.814286
39 PL2 0.488636 0.865672
40 PMP 0.48 0.854839
41 PSZ 0.477778 0.774648
42 Z98 0.477273 0.861538
43 PXP 0.466667 0.761905
44 PMH 0.465116 0.679487
45 RW2 0.462366 0.852941
46 PXG 0.462366 0.833333
47 DCS 0.455556 0.74026
48 GT1 0.454545 0.686567
49 DN9 0.447917 0.84507
50 7TS 0.444444 0.6875
51 PPE 0.444444 0.9375
52 9YM 0.44086 0.835821
53 CKT 0.436782 0.846154
54 PL8 0.427083 0.808219
55 7B9 0.418367 0.842857
56 PFM 0.413043 0.828125
57 PLP 2KZ 0.411111 0.80303
Similar Ligands (3D)
Ligand no: 1; Ligand: PL4; Similar ligands found: 1
No: Ligand Similarity coefficient
1 PL6 0.8775
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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