Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:500;
Part of Protein;
none;
submit data
39.098 K [K+]
NA A:501;
Part of Protein;
none;
submit data
22.99 Na [Na+]
PMP A:502;
Valid;
none;
Kd = 0.6 mM
248.173 C8 H13 N2 O5 P Cc1c(...
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: PMP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 PMP 1 1
2 PXP 0.7 0.888889
3 GT1 0.673077 0.793103
4 PLG 0.57377 0.866667
5 IN5 0.57377 0.912281
6 P1T 0.571429 0.825397
7 PLR 0.557692 0.781818
8 2BO 0.553846 0.881356
9 TLP 0.553846 0.881356
10 2BK 0.553846 0.881356
11 PP3 0.546875 0.881356
12 PDA 0.546875 0.881356
13 PDD 0.546875 0.881356
14 ILP 0.544118 0.852459
15 33P 0.538462 0.896552
16 IK2 0.538462 0.825397
17 5PA 0.530303 0.825397
18 PLS 0.530303 0.866667
19 PMH 0.530303 0.742857
20 PLP 0.527273 0.767857
21 C6P 0.522388 0.866667
22 PPD 0.522388 0.866667
23 ORX 0.521127 0.854839
24 PXM 0.52 0.735849
25 PZP 0.517857 0.836364
26 PLA 0.514706 0.8125
27 PY5 0.514706 0.8125
28 PL2 0.514286 0.84127
29 QLP 0.514286 0.815385
30 PE1 0.513889 0.854839
31 PPG 0.513514 0.825397
32 P0P 0.508772 0.8
33 HEY 0.507042 0.8125
34 CBA 0.5 0.83871
35 PGU 0.5 0.83871
36 7TS 0.5 0.702703
37 EA5 0.5 0.828125
38 3LM 0.5 0.787879
39 PDG 0.5 0.83871
40 7XF 0.5 0.83871
41 9YM 0.493151 0.868852
42 LCS 0.492958 0.675676
43 PMG 0.492958 0.787879
44 DCS 0.492958 0.712329
45 76U 0.486111 0.825397
46 PY6 0.486111 0.787879
47 PL4 0.48 0.854839
48 PSZ 0.479452 0.8
49 N5F 0.479452 0.825397
50 4LM 0.462687 0.725806
51 0JO 0.462687 0.714286
52 AN7 0.461538 0.741379
53 PXG 0.460526 0.866667
54 RW2 0.460526 0.8
55 FOO 0.454545 0.75
56 PL8 0.454545 0.732394
57 GLY PLP 0.454545 0.779661
58 NPL 0.45 0.898305
59 KAM 0.448718 0.825397
60 1D0 0.444444 0.8
61 7B9 0.443038 0.764706
62 2B1 0.443038 0.690141
63 P3D 0.442857 0.85
64 PLP SER 0.441176 0.779661
65 EPC 0.439394 0.789474
66 MP5 0.438596 0.728814
67 EXT 0.432836 0.79661
68 PLP PMP 0.432836 0.770492
69 AQ3 0.426829 0.8125
70 2B6 0.426829 0.662162
71 PLP ALO 0.422535 0.833333
72 MPM 0.414286 0.75
73 KOU 0.408451 0.8
74 SER PLP 0.402778 0.813559
75 HCP 0.402778 0.741935
76 PLP 2TL 0.402778 0.79661
77 Z98 0.4 0.777778
78 PFM 0.4 0.770492
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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