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Receptor
PDB id Resolution Class Description Source Keywords
2XBN 1.4 Å EC: 2.3.1.50 INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL D ECARBOXYLATIVE MECHANISM OF INACTIVATION SPHINGOMONAS PAUCIMOBILIS TRANSFERASE PYRIDOXAL PHOSPHATE
Ref.: INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL DECARBOXYLATIVE MECHANISM OF INACTIVATION. MOL.BIOSYSTEMS V. 6 1682 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:1421;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
PMP A:1420;
Valid;
none;
submit data
248.173 C8 H13 N2 O5 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XBN 1.4 Å EC: 2.3.1.50 INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL D ECARBOXYLATIVE MECHANISM OF INACTIVATION SPHINGOMONAS PAUCIMOBILIS TRANSFERASE PYRIDOXAL PHOSPHATE
Ref.: INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL DECARBOXYLATIVE MECHANISM OF INACTIVATION. MOL.BIOSYSTEMS V. 6 1682 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 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 : 2XBN; Ligand: PMP; Similar sites found with APoc: 110
This union binding pocket(no: 1) in the query (biounit: 2xbn.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 4R5Z PMP 1.3624
2 4R5Z SIN 1.3624
3 3A8U PLP 1.63934
4 6EWR PMP 1.63934
5 2OGA PGU 1.75439
6 1B9I PXG 1.80412
7 2O1O RIS 1.90217
8 2FYF PLP 2.01005
9 2HOX P1T 2.10773
10 4RKC PMP 2.26131
11 4K2M O1G 2.34192
12 2HW1 FRU 2.34899
13 4JE5 PLP 2.58449
14 4JE5 PMP 2.58449
15 5XSS XYP 2.8481
16 4FL0 PLP 3.27869
17 2CJH AKG 3.27869
18 1WYV PLP AOA 3.27869
19 1JS3 PLP 142 3.27869
20 5GVL GI8 3.27869
21 5GVL PLG 3.27869
22 5IWQ PLP 3.51288
23 1U26 IHS 3.56083
24 3PD6 PMP 3.74065
25 3PDB PMP 3.74065
26 4E3Q PMP 3.74707
27 4UHO PLP 3.74707
28 5W19 9TD 3.98126
29 1GCK ASP PLP 4.41558
30 1Y4Z PCI 4.44444
31 1OXO IK2 4.48878
32 1AJS PLA 4.61165
33 6CD1 PLG 4.68384
34 2X5F PLP 4.68384
35 6CD1 PLS 4.68384
36 6ECG PM9 4.68384
37 2HHP FLC 4.68384
38 2TPL HPP 4.68384
39 5D4Y BXP 4.91803
40 5VEQ PMP 5.10949
41 4BA5 PXG 5.38642
42 4A34 FUL 5.44218
43 1E5F PLP 5.44554
44 6CZY PMP 5.52486
45 5W71 PLP 5.62061
46 5F6U 5VK 5.73248
47 1VJO PLP 5.85242
48 5W70 9YM 5.8548
49 4M2K PLP 5.91133
50 1M7Y PPG 6.08899
51 2R5E QLP 6.32318
52 2R5C C6P 6.32318
53 1ELU PDA 6.41026
54 1PMO PLR 6.55738
55 1XI9 PLP 6.65025
56 3BWN PMP 6.90537
57 3BWN PMP PHE 6.90537
58 1GDE GLU PLP 6.94087
59 3EI9 PL6 7.49415
60 4LNL PLG 7.50751
61 4LNL 2BO 7.50751
62 4LNL 2BK 7.50751
63 1MDZ PLP 8.39695
64 1MDZ DCS 8.39695
65 1ZC9 PMP 8.8993
66 1GEX PLP HSA 9.26966
67 4ZM4 PLP 9.36768
68 3ZRR PXG 9.63542
69 2R2N PMP 9.88235
70 6FYQ PLP 10.0703
71 2ZC0 PMP 10.5651
72 4NYT PC 10.5991
73 6C74 PC 10.8108
74 1LC8 33P 10.989
75 4AOA IK2 11.2412
76 1U08 PLP 11.399
77 6DND PLP 11.4355
78 4ZSY RW2 11.4754
79 4IYO 0JO 12.0907
80 4IY7 0JO 12.0907
81 4IY7 KOU 12.0907
82 2FNU PMP UD1 13.0667
83 5M3Z PLP 13.5678
84 5M3Z PY6 13.5678
85 5M3Z NLE 13.5678
86 5YKT PMP 14.0515
87 2Z9V PXM 15.051
88 4WXG 2BO 15.2225
89 2X5D PLP 15.534
90 4HVK PMP 16.2304
91 5ZHO A2G GLA FUC 16.6667
92 1M32 PLP 17.2131
93 1CL2 PPG 19.2405
94 1UU1 PMP HSA 19.7015
95 5K8B PDG 19.8511
96 3B8X G4M 21.0256
97 3CQ5 PMP 21.4092
98 3BS8 PMP 21.5457
99 5X30 7XF 25.6281
100 5X30 4LM 25.6281
101 5X2Z 3LM 25.6281
102 3WGC PLG 31.6716
103 1LW4 PLP 31.9885
104 1LW4 TLP 31.9885
105 1DFO PLG 32.8537
106 5TXR PLP 42.1546
107 2WK9 PLG 43.9589
108 2WK9 PLP 43.9589
109 1DJ9 KAM 46.3542
110 1FC4 AKB PLP 47.3815
Pocket No.: 2; Query (leader) PDB : 2XBN; Ligand: PMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2xbn.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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