Receptor
PDB id Resolution Class Description Source Keywords
1D7R 2 Å EC: 4.1.1.64 CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA BURKHOLDERIA CEPACIA ENZYME COMPLEXES CATALYTIC MECHANISM DECARBOXYLATION INHIBITOR LYASE
Ref.: CRYSTAL STRUCTURES OF DIALKYLGLYCINE DECARBOXYLASE INHIBITOR COMPLEXES. J.MOL.BIOL. V. 294 193 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5PA A:500;
 Valid;
 none;
 submit data
332.246 C12 H17 N2 O7 P Cc1c(...
K A:436;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
NA A:435;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZC9 2 Å EC: 4.1.1.64 THE CRYSTAL STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE COMPLEX WITH PYRIDOXAMINE 5-PHOSPHATE BURKHOLDERIA CEPACIA DGD COMPLEX WITH PYRIDOXAL 5-PHOSPHATE LYASE
Ref.: ROLE OF Q52 IN CATALYSIS OF DECARBOXYLATION AND TRANSAMINATION IN DIALKYLGLYCINE DECARBOXYLASE. BIOCHEMISTRY V. 44 16392 2005
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1D7U - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
2 1M0O Ki = 4.9 mM MPM C12 H20 N2 O8 P2 CC[C@](C)(....
3 1M0N Ki = 6 mM HCP C13 H20 N2 O8 P2 Cc1c(c(c(c....
4 1M0Q Ki = 1.1 mM EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
5 1ZC9 Kd = 0.6 mM PMP C8 H13 N2 O5 P Cc1c(c(c(c....
6 1D7R - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
7 1D7S - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1D7U - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
2 1M0O Ki = 4.9 mM MPM C12 H20 N2 O8 P2 CC[C@](C)(....
3 1M0N Ki = 6 mM HCP C13 H20 N2 O8 P2 Cc1c(c(c(c....
4 1M0Q Ki = 1.1 mM EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
5 1ZC9 Kd = 0.6 mM PMP C8 H13 N2 O5 P Cc1c(c(c(c....
6 1D7R - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
7 1D7S - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6G4E - PLP ACA n/a n/a
2 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
4 6IO1 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
5 1SZS - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 1SFF - IK2 C10 H15 N2 O8 P Cc1c(c(c(c....
7 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
8 1D7U - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
9 1M0O Ki = 4.9 mM MPM C12 H20 N2 O8 P2 CC[C@](C)(....
10 1M0N Ki = 6 mM HCP C13 H20 N2 O8 P2 Cc1c(c(c(c....
11 1M0Q Ki = 1.1 mM EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
12 1ZC9 Kd = 0.6 mM PMP C8 H13 N2 O5 P Cc1c(c(c(c....
13 1D7R - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
14 1D7S - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5PA; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 5PA 1 1
2 PLG 0.632353 0.890625
3 P1T 0.628571 0.878788
4 PLS 0.611111 0.920635
5 PDA 0.605634 0.875
6 PDD 0.605634 0.875
7 PP3 0.605634 0.875
8 IK2 0.597222 0.850746
9 TLP 0.589041 0.875
10 2BO 0.589041 0.875
11 2BK 0.589041 0.875
12 IN5 0.585714 0.84375
13 PPD 0.581081 0.920635
14 C6P 0.581081 0.920635
15 PLA 0.573333 0.893939
16 PY5 0.573333 0.893939
17 PDG 0.558442 0.921875
18 PGU 0.558442 0.921875
19 7XF 0.558442 0.921875
20 CBA 0.558442 0.835821
21 ILP 0.558442 0.848485
22 33P 0.554054 0.80303
23 QLP 0.551282 0.867647
24 LPI 0.551282 0.855072
25 PMG 0.551282 0.895522
26 PMH 0.546667 0.701299
27 76U 0.544304 0.878788
28 PY6 0.544304 0.867647
29 HEY 0.544304 0.865672
30 PXP 0.538462 0.761905
31 PSZ 0.5375 0.8
32 EA5 0.5375 0.880597
33 ORX 0.5375 0.907692
34 3LM 0.5375 0.788732
35 N5F 0.5375 0.907692
36 RW2 0.536585 0.852941
37 DCS 0.531646 0.763158
38 PE1 0.530864 0.907692
39 PMP 0.530303 0.825397
40 GT1 0.522388 0.686567
41 7TS 0.518987 0.708861
42 0PR 0.518072 0.90625
43 PXG 0.518072 0.861538
44 PL4 0.518072 0.907692
45 PL2 0.5125 0.785714
46 9YM 0.512195 0.835821
47 KAM 0.505882 0.850746
48 DN9 0.5 0.84507
49 CKT 0.493506 0.846154
50 AQ3 0.483146 0.893939
51 PL8 0.476744 0.808219
52 7B9 0.465909 0.842857
53 OJQ 0.45679 0.683544
54 PLP 2KZ 0.444444 0.80303
55 PPG 0.443182 0.850746
56 LCS 0.440476 0.705128
57 RMT 0.438202 0.794118
58 PLR 0.432836 0.671875
59 1D0 0.419355 0.852941
60 PLP 0.414286 0.714286
61 AN7 0.410256 0.71875
62 PZP 0.408451 0.71875
63 0LD 0.405941 0.625
64 FOO 0.405063 0.753846
65 CAN PLP 0.404494 0.826087
66 P0P 0.402778 0.714286
67 KOU 0.402439 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: 5PA; Similar ligands found: 38
No: Ligand Similarity coefficient
1 F0G 0.9842
2 PLI 0.9837
3 0JO 0.9668
4 4LM 0.9549
5 PLP SER 0.9330
6 PLP 2TL 0.9326
7 PLP ALO 0.9312
8 SER PLP 0.9300
9 PLP CYS 0.9295
10 EVM 0.9281
11 PM9 0.9271
12 PLP GLY 0.9267
13 GLY PLP 0.9222
14 EPC 0.9214
15 L7N 0.9195
16 FEV 0.9143
17 HCP 0.9111
18 ASP PLP 0.9101
19 KET 0.9100
20 MET PLP 0.9033
21 PLP MET 0.9001
22 MPM 0.8930
23 6DF 0.8888
24 3QP 0.8876
25 PPE 0.8872
26 PLP 2ML 0.8868
27 07U 0.8843
28 PLP 0A0 0.8824
29 LEU PLP 0.8804
30 PL6 0.8799
31 PLP 999 0.8728
32 FEJ 0.8655
33 66P 0.8633
34 7CU 0.8609
35 P19 0.8593
36 IRG 0.8589
37 855 0.8585
38 EAR 0.8542
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZC9; Ligand: PMP; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 1zc9.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4UHO PLP 40.1848
2 4E3Q PMP 42.9561
3 4E3Q PMP 42.9561
4 6TOR PMP 46.6513
5 6TOR PMP 46.6513
6 6FYQ PLP 46.8822
7 6S4G PMP 47.3441
8 4ADC PLP 49.7537
9 4ADC PLP 49.7537
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