Receptor
PDB id Resolution Class Description Source Keywords
1M0N 2.2 Å EC: 4.1.1.64 STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE COMPLEXED WITH 1- AMINOCYCLOPENTANEPHOSPHONATE BURKHOLDERIA CEPACIA DECARBOXYLASE PYRIDOXAL PHOSPHATE LYASE
Ref.: AMINOPHOSPHONATE INHIBITORS OF DIALKYLGLYCINE DECAR STRUCTURAL BASIS FOR SLOW BINDING INHIBITION BIOCHEMISTRY V. 41 12320 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HCP A:434;
 Valid;
 none;
 Ki = 6 mM
394.254 C13 H20 N2 O8 P2 Cc1c(...
K A:435;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
NA A:436;
 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: HCP; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 HCP 1 1
2 EPC 0.571429 0.857143
3 EXT 0.56338 0.862069
4 4LM 0.547945 0.786885
5 0JO 0.547945 0.803279
6 PLP 0.546875 0.77193
7 F0G 0.540541 0.827586
8 MPM 0.540541 0.844828
9 PZP 0.538462 0.807018
10 FEV 0.533333 0.774194
11 KOU 0.533333 0.803279
12 EVM 0.526316 0.790323
13 P3D 0.526316 0.852459
14 6DF 0.506329 0.810345
15 PL6 0.506329 0.847458
16 FEJ 0.5 0.786885
17 Z98 0.5 0.78125
18 P89 0.494118 0.8
19 LUK 0.488372 0.671233
20 LUH 0.488372 0.671233
21 O1G 0.482759 0.753846
22 PUS 0.470588 0.690141
23 P70 0.470588 0.830508
24 PL5 0.470588 0.836066
25 AN7 0.466667 0.745763
26 GLY PLP 0.461538 0.721311
27 FOO 0.460526 0.783333
28 EQJ 0.454545 0.784615
29 5DK 0.454545 0.784615
30 PLP ABU 0.445783 0.770492
31 L7N 0.440476 0.68
32 PLP PUT 0.439024 0.790323
33 SER PLP 0.439024 0.754098
34 PLT 0.43617 0.793651
35 PLP ALO 0.433735 0.737705
36 PLR 0.432836 0.754386
37 Q0P 0.430108 0.793651
38 PLP 999 0.428571 0.737705
39 PFM 0.411765 0.746032
40 PXP 0.408451 0.733333
41 P0P 0.402778 0.741379
42 PMP 0.402778 0.741935
43 PLP PHE 0.402174 0.737705
Similar Ligands (3D)
Ligand no: 1; Ligand: HCP; Similar ligands found: 37
No: Ligand Similarity coefficient
1 TLP 0.9218
2 PLS 0.9134
3 5PA 0.9111
4 PLP 2KZ 0.9108
5 PLP BH2 0.9066
6 ILP 0.9039
7 KET 0.9028
8 PLP 2TL 0.9006
9 PY5 0.8962
10 2BK 0.8950
11 PDA 0.8928
12 2BO 0.8914
13 PLP SER 0.8906
14 PPD 0.8904
15 C6P 0.8903
16 PLA 0.8892
17 PLP CYS 0.8890
18 PM9 0.8877
19 LCS 0.8850
20 DCS 0.8838
21 PLP 2ML 0.8835
22 PPE 0.8826
23 CBA 0.8812
24 PLP 0A0 0.8793
25 P1T 0.8786
26 PP3 0.8779
27 LEU PLP 0.8776
28 PDD 0.8766
29 IN5 0.8763
30 7XF 0.8747
31 CKT 0.8738
32 PLI 0.8660
33 PGU 0.8622
34 PY6 0.8605
35 ASP PLP 0.8562
36 OJQ 0.8559
37 3QP 0.8545
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
APoc FAQ
Feedback