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Receptor
PDB id Resolution Class Description Source Keywords
5B4B 1.6 Å EC: 3.6.1.54 CRYSTAL STRUCTURE OF LPXH WITH LIPID X IN SPACEGROUP C2 PSEUDOMONAS AERUGINOSA PAO1 LPXH LIPID A LIPID X UDP-2 3-DIACYLGLUCOSAMINE HYDROLAS
Ref.: CRYSTAL STRUCTURES OF THE UDP-DIACYLGLUCOSAMINE PYROPHOSPHOHYDRASE LPXH FROM PSEUDOMONAS AERUGINOSA SCI REP V. 6 32822 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LP5 B:301;
A:301;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0;
submit data
711.861 C34 H66 N O12 P CCCCC...
GOL A:302;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5B4B 1.6 Å EC: 3.6.1.54 CRYSTAL STRUCTURE OF LPXH WITH LIPID X IN SPACEGROUP C2 PSEUDOMONAS AERUGINOSA PAO1 LPXH LIPID A LIPID X UDP-2 3-DIACYLGLUCOSAMINE HYDROLAS
Ref.: CRYSTAL STRUCTURES OF THE UDP-DIACYLGLUCOSAMINE PYROPHOSPHOHYDRASE LPXH FROM PSEUDOMONAS AERUGINOSA SCI REP V. 6 32822 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5B4A - LP5 C34 H66 N O12 P CCCCCCCCCC....
2 5B49 - LP5 C34 H66 N O12 P CCCCCCCCCC....
3 5B4B - LP5 C34 H66 N O12 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LP5; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 LP5 1 1
2 LP4 LP5 0.663366 0.911765
3 LP5 LP4 0.663366 0.911765
4 LP4 LP5 MYR DAO 0.51145 0.911765
5 U21 0.495935 0.775
6 U20 0.495935 0.775
7 PA1 PO4 FTT FTT GCS FTT PO4 KDO MYR 0.44 0.898551
8 U22 0.415385 0.777778
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5B4B; Ligand: LP5; Similar sites found with APoc: 348
This union binding pocket(no: 1) in the query (biounit: 5b4b.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2WOR 2AN None
2 3KPE TM3 None
3 5NTP 98E None
4 5N8V KZZ None
5 2VWA PTY None
6 4JMU 1ML None
7 5ET3 60C None
8 1N8V BDD None
9 1UVC STE None
10 4LWU 20U None
11 1BWO LPC None
12 3U5S FAD 0.793651
13 1TV5 N8E 0.806452
14 6BR8 PGV 1.20968
15 6BR8 6OU 1.20968
16 6AYI C3G 1.50754
17 1I0B PEL 1.6129
18 5KAU RHQ 1.81818
19 4WGF HX2 1.95122
20 3KP6 SAL 1.98676
21 3W54 RNB 2.01613
22 5IUY BOG 2.01613
23 1ZPD CIT 2.01613
24 2HFK E4H 2.01613
25 4LY9 1YY 2.01613
26 4LY9 S6P 2.01613
27 1AUA BOG 2.01613
28 3OKI OKI 2.14592
29 1FK5 OLA 2.15054
30 4R57 ACO 2.27273
31 3F8C HT1 2.38095
32 1TLG GAL 2.4
33 1NF8 BOG 2.41546
34 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 2.41935
35 2RH1 CLR 2.41935
36 2HHP FLC 2.41935
37 3R9V DXC 2.41935
38 1Q7E MET 2.41935
39 6DIO CIT 2.41935
40 3AI3 SOE 2.41935
41 2D2F ADP 2.41935
42 5V3Y 5V8 2.41935
43 4G8R 96P 2.41935
44 6BMS POV 2.41935
45 5FUS DAO 2.41935
46 2I0G I0G 2.41935
47 6F5W KG1 2.41935
48 6BMS PLM 2.41935
49 5VRH OLB 2.49042
50 3OLL EST 2.5
51 2YJD YJD 2.5
52 3SQP 3J8 2.51046
53 1H0A I3P 2.53165
54 3E3U NVC 2.53807
55 3SFI 3SF 2.54237
56 3SHZ 5CO 2.59366
57 1X0P FAD 2.7972
58 5LX9 OLB 2.82258
59 2GWH PCI 2.82258
60 1ZED PNP 2.82258
61 5C1M CLR 2.82258
62 1SJD NPG 2.82258
63 5EW9 5VC 2.82258
64 5IXK 6EW 2.82258
65 1R6N 434 2.8436
66 2E2R 2OH 2.86885
67 5XJ7 87O 2.98507
68 4XPL ACO 3.06748
69 3L1N PLM 3.09278
70 3TL1 JRO 3.14465
71 2CHT TSA 3.14961
72 2GBB CIT 3.20513
73 5AZC PGT 3.22581
74 1TMX HGX 3.22581
75 3TKY N7I 3.22581
76 4ARE FLC 3.22581
77 5DEX GLY 3.22581
78 5K53 STE 3.43511
79 3ET3 ET1 3.62903
80 3FUR Z12 3.62903
81 3G9E RO7 3.62903
82 3T03 3T0 3.62903
83 2P4Y C03 3.62903
84 2OZ5 7XY 3.62903
85 5TWO 7MV 3.62903
86 5CC2 CKA 3.62903
87 5B0I BOG 3.62903
88 3RDE OYP 3.62903
89 5MTE BB2 3.64964
90 4V2O CLQ 3.65854
91 2VDY HCY 3.75335
92 1DKF BMS 3.82979
93 5V4R MGT 4.03226
94 6BR9 PGV 4.03226
95 5MBC FMN 4.03226
96 6BR9 6OU 4.03226
97 6CB2 OLC 4.03226
98 2UW1 GVM 4.03226
99 1XMY ROL 4.03226
100 1XM4 PIL 4.03226
101 4F06 PHB 4.03226
102 5FQK 6NT 4.03226
103 2QES ADE 4.03226
104 1XMU ROF 4.03226
105 4NB5 2JT 4.09357
106 5URY PAM 4.10959
107 4HBM 0Y7 4.16667
108 3IX9 MTX 4.21053
109 4UCC ZKW 4.29185
110 2BHW NEX 4.31034
111 2BHW LUX 4.31034
112 3N7S 3N7 4.34783
113 3E85 BSU 4.43038
114 1M2Z BOG 4.43548
115 4DE3 DN8 4.43548
116 1XQP 8HG 4.43548
117 3GZ9 D32 4.43548
118 5EY0 GTP 4.43548
119 4OAR 2S0 4.43548
120 3SP6 IL2 4.43548
121 3GFZ FMN 4.43548
122 3KDU NKS 4.43548
123 3ET1 ET1 4.43548
124 3B99 U51 4.43548
125 1K7L 544 4.43548
126 5G57 6M5 4.43548
127 4X8D AVI 4.43548
128 3FEI CTM 4.43548
129 4DDY DN6 4.43548
130 1UBY DMA 4.43548
131 2FDW D3G 4.43548
132 2NPA MMB 4.43548
133 5B25 4QJ 4.43548
134 1SR7 MOF 4.43548
135 1NHZ 486 4.43548
136 3ROE THM 4.43548
137 3NJQ NJQ 4.66321
138 5DCH 1YO 4.6875
139 4X6F 3XU 4.7619
140 1UUY PPI 4.79042
141 3GF2 SAL 4.79452
142 2HJ3 FAD 4.8
143 2Z7I 742 4.83871
144 3WYJ H78 4.83871
145 5OSW DIU 4.83871
146 5OSW AE4 4.83871
147 5AHS COA 4.83871
148 3HYW DCQ 4.83871
149 5UV1 0FV 4.83871
150 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 4.83871
151 4URN NOV 4.88889
152 3G5K BB2 4.91803
153 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 5
154 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.02092
155 1GUX ASP LEU TYR CYS TYR GLU GLN LEU ASN 5.04587
156 5WL1 D3D 5.05051
157 5WL1 CUY 5.05051
158 3AB4 THR 5.05618
159 2BYC FMN 5.10949
160 4OAS 2SW 5.20833
161 5DQW ADP 5.21327
162 5CX6 CDP 5.24194
163 5HCN DAO 5.24194
164 2Q2Y MKR 5.24194
165 2Q2Y ADP 5.24194
166 5NM7 GLY 5.24194
167 1J78 VDY 5.24194
168 2WH8 II2 5.24194
169 3RY9 1CA 5.24194
170 2JHP GUN 5.24194
171 1YYE 196 5.24194
172 3LN0 52B 5.24194
173 1Q8A HCS 5.24194
174 3HR1 PF9 5.24194
175 4WOE 3S5 5.24194
176 4F4S EFO 5.26316
177 1RDT 570 5.3719
178 1RDT L79 5.3719
179 2W3L DRO 5.55556
180 6FS0 E4W 5.5814
181 3HP9 CF1 5.64516
182 6C1R EFD 5.64516
183 2P1C GG3 5.64516
184 3BOF HCS 5.64516
185 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 5.71429
186 3AQT RCO 5.71429
187 4WQ2 3SU 5.78035
188 1T0S BML 5.81395
189 1RV1 IMZ 5.88235
190 2V5E SCR 5.94059
191 4MGA 27L 6.04839
192 2BJ4 OHT 6.04839
193 4TV1 36M 6.04839
194 5AAV GW5 6.04839
195 5HYR EST 6.04839
196 1PFK ADP 6.04839
197 4TUZ 36J 6.04839
198 5WGD EST 6.04839
199 4MG7 27H 6.04839
200 6CIB ADP 6.04839
201 4MG8 27J 6.04839
202 2QE4 JJ3 6.04839
203 4MGB XDH 6.04839
204 6A46 DCM 6.04839
205 3UUD EST 6.04839
206 2O1V ADP 6.04839
207 4MGD 27N 6.04839
208 5DXE EST 6.04839
209 5WGQ EST 6.04839
210 2QA8 GEN 6.04839
211 4RJD TFP 6.06061
212 1MT1 AG2 6.19469
213 4IBF 1D5 6.20155
214 3T50 FMN 6.25
215 5IJJ I6P 6.25
216 4DOO DAO 6.34146
217 5UC4 83S 6.36364
218 5C9J DAO 6.45161
219 2JC9 ADN 6.45161
220 6MVU K4V 6.45161
221 3BJC WAN 6.45161
222 5NCB JZ3 6.45161
223 3GXO MQA 6.45161
224 5TVI MYR 6.52174
225 5M36 9SZ 6.55022
226 1ID0 ANP 6.57895
227 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 6.57895
228 2PRG BRL 6.81818
229 4V3I ASP LEU THR ARG PRO 6.85484
230 2QJY UQ2 6.95187
231 3EYK EYK 6.97674
232 3L9R L9R 7.14286
233 4B6C B5U 7.14286
234 3L9R L9Q 7.14286
235 4F7E 0SH 7.14286
236 4RC8 STE 7.20721
237 5OLK DTP 7.25806
238 5IM3 DTP 7.25806
239 3T6E UQ9 7.25806
240 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 7.28745
241 4MNS 2AX 7.54717
242 2YVE MBT 7.56757
243 2ALG DAO 7.6087
244 2ALG HP6 7.6087
245 4OGQ 7PH 7.66129
246 4OGQ 1O2 7.66129
247 6B21 C9V 7.66129
248 4OGQ SQD 7.66129
249 5OM2 DXT 7.66129
250 4OGQ UMQ 7.66129
251 5U97 PIT 7.66129
252 2WPX ACO 7.66129
253 4J25 OGA 7.66129
254 4MRP GSH 7.66129
255 4NTO 1PW 7.66129
256 6BMM OLB 7.66129
257 2WPW ACO 7.66129
258 6GMN F4E 7.69231
259 2Z9I GLY ALA THR VAL 7.71605
260 2HFN FMN 7.84314
261 1HBK COA 7.86517
262 1HBK MYR 7.86517
263 2IYG FMN 8.06452
264 1GJW GLC 8.06452
265 1WLJ U5P 8.06452
266 5J6A P46 8.06452
267 1DTL BEP 8.07453
268 1YRX FMN 8.26446
269 5KK4 44E 8.33333
270 5MWE TCE 8.57143
271 5K52 OCD 8.67924
272 3ZLR X0B 8.86076
273 4IA6 EIC 8.87097
274 1GNI OLA 8.87097
275 3SHR CMP 8.87097
276 3KO0 TFP 8.91089
277 3TDC 0EU 9.27419
278 4G86 BNT 9.27419
279 1NU4 MLA 9.27835
280 5Y02 HBX 9.34579
281 4DXD 9PC 9.67742
282 1N13 AG2 9.73451
283 2QQC AG2 9.82143
284 2QQD AG2 9.82143
285 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 9.82906
286 5A4W QCT 9.90566
287 1XVB 3BR 10.0806
288 4QO5 NAG 10.0806
289 5CHR 4NC 10.219
290 2BCG GER 10.6796
291 3B6C SDN 10.6838
292 4URX FK1 10.8871
293 2WDA L42 11.2903
294 3WH2 FLC 11.5646
295 1C9K 5GP 11.6667
296 4YSX E23 11.6935
297 2YLD CMO 11.811
298 4J6C STR 12.0968
299 2CB8 MYA 12.6437
300 2PX6 DH9 12.9032
301 4O4Z N2O 12.987
302 5U9J GER 13.0178
303 2AX9 BHM 13.3065
304 4V1F BQ1 13.9535
305 5LWY OLB 14.2857
306 4YUS FMN 14.5161
307 5OCA 9QZ 14.7059
308 5W7B MYR 14.9194
309 6BVK EAV 14.9701
310 6BVM EBV 14.9701
311 6BVI EC4 14.9701
312 6BVJ EAS 14.9701
313 6BVL EBY 14.9701
314 6D56 FVM 14.9701
315 6D59 FVJ 14.9701
316 2Q4G CIT 15.5039
317 3SCM LGN 15.7258
318 3G08 FEE 15.7258
319 3RUG DB6 15.7258
320 3QUZ QUV 15.7258
321 3E70 GDP 16.129
322 5NNT DPV 16.2162
323 4WO4 JLS 16.5323
324 4RYV ZEA 16.7742
325 4NSQ COA 16.8421
326 5YZC 95C 18.0851
327 2BO4 FLC 18.1452
328 4I67 G G G RPC 18.3908
329 2Y69 CHD 18.75
330 5VOM 9GY 19.4631
331 6CS9 PIO 19.5122
332 1TIQ COA 21.1111
333 3RMK BML 22.8916
334 3ALT MLB 22.9299
335 3HUJ AGH 23.7903
336 5W97 CHD 26.7857
337 5ZCO PEK 26.7857
338 5Z84 CHD 26.7857
339 5ZCO CHD 26.7857
340 2DYR PGV 26.7857
341 2DYS TGL 26.7857
342 5Z84 PGV 26.7857
343 5ZCO PGV 26.7857
344 2DYR TGL 26.7857
345 2DYS PGV 26.7857
346 2XN3 ID8 27.5
347 2XN5 FUN 31.4286
348 5FH7 5XL 32.2581
Pocket No.: 2; Query (leader) PDB : 5B4B; Ligand: LP5; Similar sites found with APoc: 96
This union binding pocket(no: 2) in the query (biounit: 5b4b.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 4WG0 CHD None
3 3O55 FAD 0.8
4 1FX8 BOG 1.20968
5 1C1X HFA 1.20968
6 1OQC FAD 1.6
7 1GEG GLC 1.6129
8 5EE7 5MV 2.01613
9 4IGQ OGA 2.01613
10 5G6U YJM 2.01613
11 4COL DTP 2.01613
12 5LNW HG3 2.01613
13 3BEJ MUF 2.10084
14 4RHP PEF 2.12766
15 5ICK FEZ 2.18341
16 2Q4X HMH 2.26244
17 2VCN ISZ 2.41935
18 4B1X LAB 2.41935
19 6H8S FSZ 2.41935
20 5Y79 3PG 2.41935
21 1U3R 338 2.48963
22 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 2.6087
23 1SQL GUN 2.73973
24 5C1M OLC 2.82258
25 3CB2 GDP 2.82258
26 3ETG GTP 2.82258
27 3RV5 DXC 3.37079
28 4M8E 29V 3.4632
29 4XCP PLM 3.52941
30 3O01 DXC 3.62903
31 4QCK ASD 3.62903
32 3ZPG 5GP 3.62903
33 3KMR EQN 3.62903
34 4O1Z MXM 3.62903
35 3H0A D30 3.62903
36 2HFP NSI 3.62903
37 5X13 HC4 3.7234
38 5CSD ACD 3.77358
39 4YDU ADP 3.79747
40 4DHL 0K7 4.03226
41 3RS8 ALA TRP LEU PHE GLU ALA 4.03226
42 1MO9 KPC 4.03226
43 2YFB SIN 4.03226
44 1XW6 GSH 4.12844
45 5YEE LAB 4.41176
46 2AK3 AMP 4.42478
47 5XQL C2E 4.43548
48 1II7 DA 4.43548
49 3BQD DAY 4.43548
50 1CZA ADP 4.43548
51 3T3Z 9PL 4.43548
52 1XX4 BAM 4.43548
53 1Q11 TYE 4.43548
54 5X80 SAL 5
55 1J78 OLA 5.24194
56 5HCV 60R 5.24194
57 5C2H 4PX 5.24194
58 3FAL REA 5.3719
59 6A5Y 9CR 5.46218
60 1FM9 9CR 5.46218
61 5MOB A8S 5.60345
62 2Q1H AS4 5.64516
63 2QZO KN1 6.04839
64 3UUA 0CZ 6.04839
65 6CGN DA 6.04839
66 4O08 PO6 6.04839
67 6D28 NEC 6.04839
68 4OB6 S2T 6.04839
69 3P9T TCL 6.39269
70 4PEG 5GP 6.45161
71 5TVI O8N 6.52174
72 5M37 9SZ 6.52174
73 6C0B PAM 6.85484
74 3RLF MAL 7.66129
75 5A86 D7E 7.66129
76 5OKL PAM 8.06452
77 2X1L MET 8.06452
78 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 8.06452
79 2CDO GAL AAL GAL AAL GAL AAL 8.125
80 3ZVS MLI 8.125
81 1YC4 43P 8.33333
82 1MID LAP 8.79121
83 5X3R 7Y3 9.26829
84 3GQT UFO 9.27419
85 3WUD GLC GAL 9.55882
86 4ZGM 32M 10.6557
87 5V49 MET 10.8871
88 3WFD AXO 10.9589
89 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 11.2245
90 2ZJ5 ADP 11.2903
91 1S14 NOV 11.3402
92 2ZO9 MLI 12.9032
93 4V1T ADP 14.1129
94 3CV2 COA 14.9194
95 2O1O RIS 16.129
96 5IHE D5M 22.9839
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