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
Ligand no: 1; Ligand: PL4; Similar ligands found: 55
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 PDG 0.733333 0.952381
9 7XF 0.733333 0.952381
10 PGU 0.733333 0.952381
11 PLS 0.726027 0.920635
12 LPI 0.723684 0.882353
13 C6P 0.693333 0.920635
14 PPD 0.693333 0.920635
15 PDD 0.631579 0.875
16 PDA 0.631579 0.875
17 PP3 0.631579 0.875
18 ILP 0.625 0.876923
19 2BO 0.615385 0.875
20 TLP 0.615385 0.875
21 2BK 0.615385 0.875
22 AQ3 0.595506 0.865672
23 76U 0.571429 0.907692
24 IN5 0.571429 0.84375
25 EA5 0.564706 0.938462
26 PLG 0.551282 0.890625
27 KAM 0.550562 0.907692
28 P1T 0.55 0.878788
29 CBA 0.547619 0.835821
30 IK2 0.52439 0.850746
31 PLA 0.52381 0.865672
32 5PA 0.518072 0.907692
33 PL5 0.516854 0.859375
34 33P 0.506024 0.80303
35 PMG 0.505747 0.895522
36 LLP 0.5 0.90625
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 7TS 0.444444 0.6875
50 PPE 0.444444 0.9375
51 9YM 0.44086 0.835821
52 PL8 0.427083 0.808219
53 7B9 0.418367 0.842857
54 PFM 0.413043 0.828125
55 PLP 2KZ 0.411111 0.80303
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: 5
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 4R5Z PMP 16.8937
4 5VEQ PMP 23.601
5 2X5D PLP 39.5631
Pocket No.: 2; Query (leader) PDB : 3EI9; Ligand: PL6; Similar sites found with APoc: 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 Sequence Similarity
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