Receptor
PDB id Resolution Class Description Source Keywords
1m0q 2 Å EC: 4.1.1.64 STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE COMPLEXED WITH S-1 AMINOETHANEPHOSPHONATE 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
EPC A:435;
 Valid;
 none;
 Ki = 1.1 mM
354.19 C10 H16 N2 O8 P2 Cc1c(...
K A:434;
 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: EPC; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 EPC 1 1
2 F0G 0.714286 0.960784
3 KOU 0.676923 0.857143
4 6DF 0.661765 0.941176
5 FEJ 0.652174 0.907407
6 PL6 0.637681 0.872727
7 EXT 0.615385 0.888889
8 PL5 0.608108 0.827586
9 P70 0.608108 0.888889
10 PLP 0.603448 0.862745
11 0JO 0.597015 0.857143
12 4LM 0.597015 0.907407
13 PZP 0.59322 0.901961
14 MPM 0.588235 0.942308
15 PUS 0.586667 0.727273
16 5DK 0.584416 0.774194
17 EQJ 0.584416 0.774194
18 FEV 0.57971 0.890909
19 EVM 0.571429 0.842105
20 HCP 0.571429 0.857143
21 P3D 0.571429 0.783333
22 Z98 0.561644 0.8
23 PLT 0.554217 0.813559
24 PLP ALO 0.547945 0.851852
25 SER PLP 0.534247 0.803571
26 Q0P 0.53012 0.813559
27 AN7 0.529412 0.830189
28 PLP 999 0.52 0.818182
29 FOO 0.5 0.87037
30 P89 0.493827 0.790323
31 LUH 0.487805 0.705882
32 LUK 0.487805 0.705882
33 PLP PHE 0.481928 0.785714
34 O1G 0.481928 0.8
35 GLY PLP 0.479452 0.8
36 PLR 0.47541 0.88
37 PLP PUT 0.473684 0.75
38 PLP ABU 0.461538 0.758621
39 P0P 0.461538 0.826923
40 PFM 0.461538 0.793103
41 IN5 0.458333 0.810345
42 PLP MYB 0.453488 0.686567
43 PXP 0.446154 0.781818
44 PLP PVH 0.443182 0.734375
45 PMP 0.439394 0.789474
46 L7N 0.4375 0.666667
47 GT1 0.432836 0.785714
48 PP3 0.421053 0.783333
49 PDA 0.421053 0.783333
50 PDD 0.421053 0.783333
51 2BK 0.410256 0.783333
52 PLS 0.410256 0.741935
53 TLP 0.410256 0.783333
54 2BO 0.410256 0.783333
55 C6P 0.405063 0.741935
Similar Ligands (3D)
Ligand no: 1; Ligand: EPC; Similar ligands found: 22
No: Ligand Similarity coefficient
1 IK2 0.9482
2 PLP AOA 0.9482
3 PLG 0.9406
4 PLI 0.9376
5 DCS 0.9361
6 P1T 0.9361
7 OJQ 0.9338
8 PLP GLY 0.9331
9 5PA 0.9214
10 PMH 0.9205
11 PLP 2TL 0.9177
12 PLP SER 0.9161
13 LCS 0.9154
14 7TS 0.9148
15 PLP CYS 0.8987
16 CKT 0.8823
17 PY5 0.8791
18 ASP PLP 0.8752
19 PPD 0.8752
20 7XF 0.8734
21 ILP 0.8734
22 3LM 0.8572
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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