Receptor
PDB id Resolution Class Description Source Keywords
1M0O 2.4 Å EC: 4.1.1.64 STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE COMPLEXED WITH 1-A METHYLPROPANEPHOSPHONATE 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
K A:435;
Part of Protein;
none;
submit data
39.098 K [K+]
MPM A:434;
Valid;
none;
Ki = 4.9 mM
382.243 C12 H20 N2 O8 P2 CC[C@...
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: MPM; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 MPM 1 1
2 EPC 0.588235 0.942308
3 EXT 0.57971 0.875
4 FEV 0.569444 0.877193
5 PLP 0.564516 0.814815
6 4LM 0.56338 0.859649
7 0JO 0.56338 0.844828
8 PZP 0.555556 0.851852
9 F0G 0.555556 0.907407
10 KOU 0.547945 0.844828
11 EVM 0.540541 0.830508
12 P3D 0.540541 0.774194
13 HCP 0.540541 0.844828
14 AN7 0.521127 0.785714
15 6DF 0.519481 0.888889
16 PL6 0.519481 0.859649
17 FOO 0.513889 0.824561
18 FEJ 0.512821 0.859649
19 Z98 0.512821 0.790323
20 P89 0.506024 0.809524
21 LUH 0.5 0.7
22 PUS 0.5 0.720588
23 LUK 0.5 0.7
24 O1G 0.494118 0.761905
25 EQJ 0.482353 0.765625
26 5DK 0.482353 0.765625
27 P70 0.481928 0.875
28 PL5 0.481928 0.816667
29 L7N 0.469136 0.662162
30 PFM 0.45679 0.783333
31 GLY PLP 0.454545 0.758621
32 PLP PUT 0.45 0.741935
33 PLR 0.446154 0.830189
34 PXP 0.441176 0.741379
35 Q0P 0.43956 0.803279
36 PLP ABU 0.439024 0.75
37 SER PLP 0.432099 0.793103
38 PLT 0.430108 0.803279
39 PLP ALO 0.426829 0.807018
40 PLP 999 0.421687 0.775862
41 PMP 0.414286 0.75
42 P0P 0.414286 0.781818
43 GT1 0.408451 0.775862
44 PLP MYB 0.402174 0.731343
Similar Ligands (3D)
Ligand no: 1; Ligand: MPM; Similar ligands found: 35
No: Ligand Similarity coefficient
1 PLS 0.9224
2 TLP 0.9209
3 PP3 0.9172
4 PLP SER 0.9156
5 PDA 0.9152
6 PDD 0.9144
7 IN5 0.9118
8 PLG 0.9069
9 PLI 0.9027
10 2BK 0.9022
11 C6P 0.9002
12 DCS 0.8977
13 2BO 0.8958
14 P1T 0.8934
15 5PA 0.8930
16 PLP CYS 0.8914
17 CKT 0.8914
18 PLP 2TL 0.8903
19 PLP 2ML 0.8889
20 ILP 0.8889
21 IK2 0.8888
22 PLP GLY 0.8843
23 7TS 0.8831
24 LCS 0.8769
25 PLA 0.8723
26 7XF 0.8714
27 OJQ 0.8697
28 PMH 0.8680
29 PY5 0.8661
30 PLP 2KZ 0.8658
31 PPD 0.8640
32 ASP PLP 0.8629
33 KET 0.8628
34 3QP 0.8580
35 PLP 0A0 0.8577
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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