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: 83
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 2BK 0.553846 0.881356
9 2BO 0.553846 0.881356
10 TLP 0.553846 0.881356
11 PDD 0.546875 0.881356
12 PP3 0.546875 0.881356
13 PDA 0.546875 0.881356
14 ILP 0.544118 0.852459
15 IK2 0.538462 0.825397
16 33P 0.538462 0.896552
17 PMH 0.530303 0.742857
18 5PA 0.530303 0.825397
19 PLS 0.530303 0.866667
20 PLP 0.527273 0.767857
21 PPD 0.522388 0.866667
22 C6P 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 PDG 0.5 0.83871
35 CBA 0.5 0.83871
36 EA5 0.5 0.828125
37 3LM 0.5 0.787879
38 7XF 0.5 0.83871
39 7TS 0.5 0.702703
40 PGU 0.5 0.83871
41 9YM 0.493151 0.868852
42 DCS 0.492958 0.712329
43 PMG 0.492958 0.787879
44 LPI 0.492958 0.776119
45 LCS 0.492958 0.675676
46 76U 0.486111 0.825397
47 PY6 0.486111 0.787879
48 PL4 0.48 0.854839
49 PSZ 0.479452 0.8
50 N5F 0.479452 0.825397
51 0JO 0.462687 0.714286
52 4LM 0.462687 0.725806
53 AN7 0.461538 0.741379
54 PXG 0.460526 0.866667
55 RW2 0.460526 0.8
56 FOO 0.454545 0.75
57 PL8 0.454545 0.732394
58 NPL 0.45 0.898305
59 FEV 0.449275 0.714286
60 KAM 0.448718 0.825397
61 RMT 0.448718 0.765625
62 1D0 0.444444 0.8
63 2B1 0.443038 0.690141
64 7B9 0.443038 0.764706
65 P3D 0.442857 0.85
66 EVM 0.442857 0.786885
67 EPC 0.439394 0.789474
68 MP5 0.438596 0.728814
69 PLP CYS 0.43662 0.836066
70 EXT 0.432836 0.79661
71 AQ3 0.426829 0.8125
72 2B6 0.426829 0.662162
73 MPM 0.414286 0.75
74 F0G 0.414286 0.762712
75 PLP 2TL 0.410959 0.85
76 KOU 0.408451 0.8
77 PLP SEP 0.405405 0.85
78 PLP BH2 0.405405 0.85
79 SEP PLP 0.405405 0.85
80 HCP 0.402778 0.741935
81 LEU PLP 0.4 0.822581
82 Z98 0.4 0.777778
83 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 with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 1zc9.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3A8U PLP 38.3372
2 4UHO PLP 40.1848
3 6FYQ PLP 46.8822
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