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 (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1SZS - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 1SFF - IK2 C10 H15 N2 O8 P Cc1c(c(c(c....
3 1D7U - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
4 1M0O Ki = 4.9 mM MPM C12 H20 N2 O8 P2 CC[C@](C)(....
5 1M0N Ki = 6 mM HCP C13 H20 N2 O8 P2 Cc1c(c(c(c....
6 1M0Q Ki = 1.1 mM EPC C10 H16 N2 O8 P2 Cc1c(c(c(c....
7 1ZC9 Kd = 0.6 mM PMP C8 H13 N2 O5 P Cc1c(c(c(c....
8 1D7R - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
9 1D7S - DCS C11 H16 N3 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HCP; Similar ligands found: 30
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 MPM 0.540541 0.844828
8 PZP 0.538462 0.807018
9 KOU 0.533333 0.803279
10 P3D 0.526316 0.852459
11 PL6 0.506329 0.847458
12 6DF 0.506329 0.810345
13 Z98 0.5 0.78125
14 P89 0.494118 0.8
15 O1G 0.482759 0.753846
16 PUS 0.470588 0.690141
17 LLP 0.470588 0.825397
18 PL5 0.470588 0.836066
19 AN7 0.466667 0.745763
20 FOO 0.460526 0.783333
21 5DK 0.454545 0.784615
22 PLP ABU 0.445783 0.770492
23 PLP PUT 0.439024 0.810345
24 PLT 0.43617 0.793651
25 PLR 0.432836 0.754386
26 PFM 0.411765 0.746032
27 PXP 0.408451 0.733333
28 PMP 0.402778 0.741935
29 P0P 0.402778 0.741379
30 PLP PHE 0.402174 0.737705
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZC9; Ligand: PMP; Similar sites found: 78
This union binding pocket(no: 1) in the query (biounit: 1zc9.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JQY A32 0.01297 0.41514 None
2 2HHP FLC 0.005738 0.46644 1.38568
3 1GCK ASP PLP 0.008193 0.40059 1.55844
4 1FC4 AKB PLP 0.003524 0.41298 1.74564
5 2FYF PLP 0.004953 0.43137 1.75879
6 1CL2 PPG 0.004342 0.4041 1.77215
7 4ORM FMN 0.03723 0.40698 1.99501
8 4ORM 2V6 0.03723 0.40698 1.99501
9 4ORM ORO 0.03723 0.40698 1.99501
10 5W70 9YM 0.0007734 0.44339 2.02247
11 1K1Y MAL 0.01555 0.42541 2.07852
12 5U23 TQP 0.0009156 0.45715 2.09424
13 4IY7 KOU 0.001647 0.42132 2.267
14 4ZAH T5K 0.0003514 0.4064 2.27273
15 1MDZ DCS 0.004654 0.42759 2.29008
16 1MDZ PLP 0.004728 0.42605 2.29008
17 1M32 PLP 0.009788 0.42192 2.45902
18 5GVL GI8 0.01761 0.4072 2.77136
19 5GVL PLG 0.01761 0.4072 2.77136
20 1E5F PLP 0.001541 0.43675 2.9703
21 3VP6 HLD 0.0002014 0.43068 3.00231
22 1VJO PLP 0.002076 0.43094 3.30789
23 1LW4 PLP 0.00002164 0.49236 3.45821
24 1LW4 TLP 0.00005295 0.49125 3.45821
25 1ELU PDA 0.002705 0.41791 4.10256
26 1ELU CSS 0.003161 0.40406 4.10256
27 3ZRR PXG 0.0006464 0.43699 4.42708
28 2VUZ NAG BMA NAG MAN MAN NAG NAG 0.01915 0.40736 4.65116
29 4LNL PLG 0.0001391 0.48922 4.8048
30 4LNL 2BO 0.0002304 0.47379 4.8048
31 5X2Z 3LM 0.0005942 0.45781 5.02513
32 5X30 7XF 0.0006563 0.44433 5.02513
33 5X30 4LM 0.0008284 0.44431 5.02513
34 1B9I PXG 0.0006433 0.41778 5.15464
35 1U08 PLP 0.004476 0.42875 5.44041
36 1DFO PLG 0.002078 0.42484 5.51559
37 4X1Z FUC GAL NDG 0.02085 0.40185 5.72289
38 2Z9V PXM 0.0004286 0.49044 6.88775
39 2OGA PGU 0.001373 0.43458 7.01754
40 5W71 9YM 0.001 0.46655 7.04545
41 5W71 PLP 0.0001537 0.46467 7.04545
42 1V1A KDG 0.01044 0.41532 7.11974
43 4M2K PLP 0.006172 0.42664 7.63547
44 2X5F PLP 0.01415 0.40457 7.67442
45 2XBN PMP 0.0007003 0.45464 8.8993
46 1WYV PLP AOA 0.004791 0.41084 8.90411
47 5DJ3 5DK 0.003633 0.41241 9.30851
48 4K2M O1G 0.0002153 0.44114 9.93072
49 3PD6 PMP 0.002505 0.44091 10.7232
50 3PDB PMP 0.003984 0.42662 10.7232
51 3WGC PLG 0.0002016 0.47639 11.7302
52 1DJ9 KAM 0.00111 0.44315 13.8021
53 5LZH 7BO 0.0184 0.40306 14.5631
54 5K8B PDG 0.0003825 0.46072 15.6328
55 5DDW 5B6 0.00000005386 0.59001 24.7113
56 4AOA IK2 0.00000012 0.62105 25.4042
57 4ZM4 PLP 0.0000003473 0.60867 29.5612
58 4ZM4 P3B 0.000005079 0.5239 29.5612
59 2YKX AKG 0.004702 0.43445 30.485
60 3BS8 PMP 0.00000000682 0.69769 35.1039
61 5KGS 6SR 0.0000002619 0.63871 35.2298
62 3FQ8 PMP 0.0000008961 0.57817 36.2998
63 4ZSY RW2 0.000000009487 0.62124 36.7206
64 3A8U PLP 0.0000000005146 0.58487 38.3372
65 4UHO PLP 0.000000002174 0.75919 40.1848
66 1MLY ACZ PLP 0.0000006645 0.57284 40.3263
67 2CJH AKG 0.0000000006914 0.72148 40.6467
68 4E3Q PMP 0.00000001755 0.68925 42.9561
69 4B98 PXG 0.00000002257 0.64452 43.8799
70 2OAT PFM 0.0000003856 0.59045 45.0346
71 4UOX PLP 0.00000001547 0.68097 45.7275
72 4UOX PUT 0.0000002278 0.60856 45.7275
73 4UOX PLP PUT 0.0000005944 0.58221 45.7275
74 4BA5 PXG 0.0000004354 0.59594 47.3441
75 5G09 6DF 0.00000006553 0.61923 48.7298
76 5WYF ILP 0.00000009002 0.61328 49.1917
77 4ADC PLP 0.00000005906 0.56318 49.7537
78 5G4J EXT 0.000002205 0.55049 49.8845
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