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: 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 : 2XBN; Ligand: PMP; Similar sites found: 219
This union binding pocket(no: 1) in the query (biounit: 2xbn.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZJ6 G3D 0.004239 0.4125 1.06952
2 1R6D DAU 0.005393 0.40142 1.48368
3 1F1V DHY 0.01082 0.40495 1.54799
4 3A8U PLP 0.009921 0.43195 1.63934
5 1UF5 CDT 0.006258 0.41023 1.65016
6 3SHR CMP 0.005613 0.41213 1.67224
7 3L6R MLI 0.02506 0.40826 1.7341
8 3MTW M3R 0.0009883 0.42752 1.73697
9 1B9I PXG 0.002198 0.41858 1.80412
10 3P7I P7I 0.001714 0.44389 1.86916
11 2O1O RIS 0.03723 0.40248 1.90217
12 4LIT AKG 0.006164 0.42538 1.9656
13 2FYF PLP 0.01066 0.42467 2.01005
14 4W6Z ETF 0.002113 0.47566 2.01729
15 1Z41 FMN 0.005307 0.40057 2.07101
16 3ZPG 5GP 0.03576 0.41223 2.09424
17 3DGB MUC 0.005135 0.40925 2.09424
18 2ZWS PLM 0.002715 0.48983 2.10773
19 2HOX P1T 0.002183 0.43272 2.10773
20 2GWD GLU 0.01087 0.40486 2.10773
21 2Y7G AAE 0.002493 0.41269 2.12766
22 2O66 FLC 0.01014 0.41578 2.22222
23 1TOI HCI 0.00004136 0.44396 2.27273
24 1HQL GLA MBG 0.03946 0.40066 2.33463
25 4K2M O1G 0.006238 0.40289 2.34192
26 2HW1 FRU 0.0324 0.40515 2.34899
27 1QDS PGA 0.007528 0.40699 2.39044
28 1V6A TRE 0.02019 0.40246 2.40964
29 4M5P 23W 0.04718 0.40018 2.457
30 1UW1 ADP 0.01638 0.40652 2.5
31 2BZ1 TAU 0.01014 0.45758 2.55102
32 4JE5 PLP 0.005927 0.43304 2.58449
33 4JE5 PMP 0.006368 0.43149 2.58449
34 2EB5 OXL 0.001932 0.45422 2.62172
35 1I0Z OXM 0.02115 0.4241 2.7027
36 1Y1A GSH 0.003105 0.49106 2.73224
37 2JFV FLC 0.009815 0.42184 2.74914
38 4IXW IXW 0.005983 0.41566 2.75591
39 3L24 GOA 0.0274 0.41826 2.8103
40 1S8F GDP 0.003827 0.40991 2.82486
41 3LTW HLZ 0.01223 0.41744 2.85714
42 2C5S AMP 0.001242 0.44401 2.90557
43 2WGC SIA GAL BGC 0.001263 0.50854 2.92398
44 1WGC SIA GAL BGC 0.02353 0.42881 2.92398
45 4B16 NAG 0.002338 0.48282 3.00752
46 3CEV ARG 0.01128 0.4042 3.01003
47 1T10 F6P 0.002828 0.44038 3.0445
48 4IHQ ADP 0.01333 0.40117 3.0445
49 1SBZ FMN 0.001107 0.4044 3.04569
50 2VAR KDF 0.008339 0.401 3.19489
51 2VAR KDG 0.008446 0.40078 3.19489
52 4COQ SAN 0.00545 0.43358 3.23887
53 2BO4 FLC 0.00931 0.42883 3.27456
54 4FL0 PLP 0.001363 0.45965 3.27869
55 2CJH AKG 0.002452 0.43844 3.27869
56 2ZJ5 ADP 0.003254 0.43768 3.27869
57 1WYV PLP AOA 0.00561 0.41805 3.27869
58 1JS3 PLP 142 0.005481 0.41495 3.27869
59 5T4J PLP ABU 0.004705 0.4065 3.28767
60 1YHM AHD 0.00119 0.45701 3.31492
61 1Y42 TYR 0.01313 0.40595 3.31633
62 3E5P PPI 0.02919 0.43953 3.50404
63 3DG6 MUC 0.005917 0.40272 3.54223
64 3SQG COM 0.01419 0.44069 3.58423
65 2Q8H TF4 0.007187 0.44832 3.6855
66 3PD6 PMP 0.0003595 0.49349 3.74065
67 3PDB PMP 0.0004273 0.48406 3.74065
68 2IZ1 ATR 0.002508 0.44903 3.74707
69 4E3Q PMP 0.005137 0.43613 3.74707
70 3K3G MMU 0.006207 0.42254 3.82353
71 1RZM PEP 0.003462 0.43081 3.84615
72 1RZM E4P 0.01775 0.41545 3.84615
73 2Y6P CTP 0.0112 0.40003 3.84615
74 1RYI GOA 0.02549 0.43006 3.9267
75 4WBD ADP 0.005727 0.43888 3.98126
76 2CE7 ADP 0.001257 0.42828 3.98126
77 4WBD CIT 0.02526 0.4138 3.98126
78 2B7N NTM 0.02206 0.40075 3.98126
79 1CTU ZEB 0.002861 0.40648 4.08163
80 2QV7 ADP 0.001732 0.41853 4.1543
81 4E1M TQ2 0.006073 0.41075 4.21687
82 1SQ5 PAU 0.006815 0.4182 4.22078
83 3F81 STT 0.03089 0.41555 4.37158
84 4K30 NLG 0.01789 0.40016 4.375
85 1C0I BE2 0.002712 0.40634 4.40771
86 1C0I FAD 0.002712 0.40634 4.40771
87 1GCK ASP PLP 0.003829 0.41836 4.41558
88 1SC3 MLI 0.01098 0.4318 4.49438
89 1VDC FAD 0.003145 0.406 4.5045
90 3TKA CTN 0.002838 0.51042 4.61095
91 1AJS PLA 0.003216 0.41179 4.61165
92 2XDQ MGX 0.006479 0.45064 4.68384
93 2X5F PLP 0.003352 0.44535 4.68384
94 2HHP FLC 0.03726 0.40861 4.68384
95 2TPL HPP 0.003 0.40704 4.68384
96 4HZO COA 0.01168 0.40815 4.71698
97 1Y7P RIP 0.02386 0.41503 4.93274
98 1PEA ACM 0.002531 0.4633 4.93506
99 1KTC NGA 0.006581 0.41885 4.93827
100 4NC7 I3C 0.009258 0.42895 5.05051
101 3E2Y PMP 0.0005677 0.47808 5.12195
102 1H16 DTL 0.0005494 0.50572 5.15223
103 4KCT PYR 0.003214 0.42687 5.15223
104 1H16 PYR 0.02165 0.41714 5.15223
105 4LO6 SIA GAL 0.02205 0.41377 5.26316
106 1M5B BN1 0.004046 0.40873 5.32319
107 3W8S GSH 0.01305 0.41091 5.33981
108 3BHO B4P 0.0104 0.44798 5.38642
109 4RJK PYR 0.008152 0.43819 5.38642
110 4BA5 PXG 0.00455 0.42599 5.38642
111 1E5F PLP 0.000004195 0.56655 5.44554
112 1WRA PC 0.03294 0.40255 5.51948
113 1BTN I3P 0.001224 0.51369 5.66038
114 1VJO PLP 0.002122 0.44135 5.85242
115 4M2K PLP 0.0002379 0.50879 5.91133
116 3S9K CIT 0.004632 0.47518 5.9322
117 1QH9 LAC 0.01294 0.41631 6.03448
118 4O8A 2OP 0.0002339 0.52475 6.11354
119 1NU4 MLA 0.002538 0.48091 6.18557
120 3QDY A2G GAL 0.004829 0.44944 6.29371
121 3QDT A2G GAL 0.006092 0.44445 6.29371
122 3QDY CBS 0.01977 0.4132 6.29371
123 3I51 45C 0.001905 0.42608 6.2963
124 2R5C C6P 0.001409 0.43725 6.32318
125 2R5E QLP 0.001855 0.43206 6.32318
126 1UCN ADP 0.006233 0.40186 6.32318
127 1Q11 TYE 0.01307 0.40604 6.45161
128 3TFC PEP 0.001732 0.4437 6.49351
129 1XI9 PLP 0.005554 0.43913 6.65025
130 1ULE GLA GAL NAG 0.01187 0.43011 6.66667
131 2E1A MSE 0.003316 0.4263 6.66667
132 4E28 9MZ 0.02094 0.40666 6.76923
133 4E28 0MZ 0.01734 0.40541 6.76923
134 3O2K QRP 0.003374 0.42103 6.79157
135 1WDA BAG 0.009924 0.40651 6.79157
136 3QV9 QV7 0.02191 0.40088 6.79157
137 4EXO PYR 0.02578 0.41335 6.84932
138 2Y7P SAL 0.002434 0.43737 6.88073
139 1H0C AOA 0.008161 0.43156 6.88775
140 3BWN PMP 0.000231 0.49701 6.90537
141 3BWN PMP PHE 0.001877 0.4282 6.90537
142 1GDE GLU PLP 0.007998 0.40765 6.94087
143 4NAO AKG 0.008824 0.42994 7.36196
144 3EI9 PL6 0.002923 0.41349 7.49415
145 4LNL PLG 0.0008381 0.46482 7.50751
146 4LNL 2BO 0.0008875 0.45889 7.50751
147 4LNL 2BK 0.000002649 0.4387 7.50751
148 1XE7 GUN 0.01136 0.43807 7.88177
149 3MD0 GDP 0.00494 0.41912 7.88732
150 1T0S BML 0.01473 0.42545 8.13953
151 1MDZ DCS 0.000006522 0.47578 8.39695
152 1MDZ PLP 0.000005747 0.47578 8.39695
153 3GTD MLI 0.01562 0.40743 8.43091
154 1Y75 NAG 0.008754 0.40878 8.47458
155 2YLD CMO 0.01245 0.41708 8.66142
156 1G8S MET 0.01287 0.41643 8.69565
157 1O9U ADZ 0.01211 0.43664 8.85714
158 2VKL MLT 0.014 0.44102 8.88889
159 1ZC9 PMP 0.0007003 0.45464 8.8993
160 1GEX PLP HSA 0.003419 0.4048 9.26966
161 2HVK TBA 0.009911 0.42165 9.43396
162 3MAG 3MA 0.0468 0.41252 9.44625
163 3ZRR PXG 0.005829 0.41041 9.63542
164 2R2N PMP 0.001709 0.45489 9.88235
165 2QCX PF1 0.01991 0.40273 9.88593
166 4F8L GAL 0.00542 0.47293 10.3448
167 1H8G CHT 0.02476 0.43562 10.5263
168 4AF5 CIT 0.0212 0.40642 10.5263
169 2ZC0 PMP 0.0002416 0.47997 10.5651
170 1JH7 UVC 0.004211 0.43272 10.582
171 4NYT PC 0.02343 0.40984 10.5991
172 2JGS BTN 0.004314 0.42943 10.7692
173 4JCA CIT 0.001331 0.49596 10.7784
174 1C1L GAL BGC 0.005468 0.43984 10.9489
175 1LC8 33P 0.0003104 0.44042 10.989
176 4AOA IK2 0.008995 0.41224 11.2412
177 1U08 PLP 0.002747 0.44964 11.399
178 1XX4 BAM 0.02572 0.41969 11.4943
179 9LDT OXM 0.009865 0.44921 11.747
180 1A59 CIT 0.02352 0.40958 11.9048
181 3BY8 MLT 0.01231 0.42305 11.9718
182 4IYO 0JO 0.00004981 0.50035 12.0907
183 4IY7 0JO 0.00005357 0.49898 12.0907
184 4IY7 KOU 0.00006319 0.49586 12.0907
185 1V7R CIT 0.03966 0.41646 12.3656
186 2WQF FMN 0.007511 0.40278 12.3762
187 1YOA FMN 0.0009316 0.51596 12.5786
188 3U1T MLI 0.002265 0.45804 13.2686
189 3R51 MMA 0.002862 0.4689 13.75
190 1SS4 GSH 0.001762 0.50693 14.3791
191 1LNX URI 0.001804 0.44294 14.8148
192 1EB9 HBA 0.002308 0.42282 14.8855
193 4CCO OGA 0.009952 0.41113 15
194 2Z9V PXM 0.01222 0.42619 15.051
195 2X5D PLP 0.0006266 0.49505 15.534
196 2V5E SCR 0.001741 0.4897 15.8416
197 4HVK PMP 0.0000522 0.5423 16.2304
198 2VQ5 HBA 0.002909 0.45287 16.4179
199 2VQ5 LDP 0.0315 0.4151 16.4179
200 1M32 PLP 0.01709 0.41899 17.2131
201 2WCI GSH 0.007258 0.42224 18.5185
202 1CL2 PPG 0.0006439 0.45204 19.2405
203 3KPE TM3 0.02551 0.4027 19.6078
204 1UU1 PMP HSA 0.002246 0.42488 19.7015
205 1ECM TSA 0.009705 0.40692 21.1009
206 3CQ5 PMP 0.0001453 0.52681 21.4092
207 3BS8 PMP 0.005836 0.429 21.5457
208 4OHB 5HM 0.003039 0.40952 21.5789
209 3GM5 CIT 0.02224 0.40546 22.6415
210 1GU3 BGC BGC BGC BGC BGC 0.003668 0.42974 25.5034
211 5X30 7XF 0.00821 0.43466 25.6281
212 5X30 4LM 0.01478 0.42538 25.6281
213 3WGC PLG 0.0004807 0.47122 31.6716
214 1DFO PLG 0.0005368 0.45547 32.8537
215 2XD9 XD9 0.002964 0.44486 42.515
216 2WK9 PLG 0.0000006831 0.50202 43.9589
217 2WK9 PLP 0.000002197 0.49876 43.9589
218 1DJ9 KAM 0.00000003599 0.66223 46.3542
219 1FC4 AKB PLP 0.00000264 0.56217 47.3815
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