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Receptor
PDB id Resolution Class Description Source Keywords
1S17 1.95 Å EC: 3.5.1.88 IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE PSEUDOMONAS AERUGINOSA PEPTIDE DEFORMYLASE INHIBITOR RATIONAL DRUG DESIGN ANTIBIOPROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEF INHIBITORS BIOORG.MED.CHEM.LETT. V. 14 1477 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNR A:501;
B:601;
Valid;
Valid;
none;
none;
ic50 < 5 nM
238.263 C10 H10 N2 O3 S c1ccc...
GOL A:401;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI A:301;
B:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1S17 1.95 Å EC: 3.5.1.88 IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE PSEUDOMONAS AERUGINOSA PEPTIDE DEFORMYLASE INHIBITOR RATIONAL DRUG DESIGN ANTIBIOPROTEIN-LIGAND COMPLEX HYDROLASE
Ref.: IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEF INHIBITORS BIOORG.MED.CHEM.LETT. V. 14 1477 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
2 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
8 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
8 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
9 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
11 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
12 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GNR 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1S17; Ligand: GNR; Similar sites found with APoc: 299
This union binding pocket(no: 1) in the query (biounit: 1s17.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5UGW GSH None
2 1ZEI CRS None
3 2VWA PTY None
4 1UO4 PIH None
5 4WG0 CHD None
6 5NNT DPV None
7 1UY4 XYP XYP XYP XYP None
8 6BOC EU7 None
9 3KIF GDL None
10 6BOC RIM None
11 4OB6 S2T None
12 1MT1 AG2 None
13 1UO5 PIH None
14 6BKK 308 None
15 4XU6 TDA None
16 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO None
17 3UEC ALA ARG TPO LYS None
18 1PVN MZP None
19 5MWE TCE None
20 5C2N NAG None
21 3V78 ET None
22 2ALG HP6 None
23 2ALG DAO None
24 1R6N 434 1.66667
25 2J83 BAT 1.66667
26 4MRP GSH 1.66667
27 1M2Z BOG 1.66667
28 3ZZH NLG 1.66667
29 1WLJ U5P 1.66667
30 5NM7 GLY 1.66667
31 2JJK R15 1.66667
32 2Q37 3AL 1.66667
33 1ATL 0QI 2.22222
34 4V3I ASP LEU THR ARG PRO 2.22222
35 4XNV BUR 2.22222
36 3SQP 3J8 2.22222
37 6H8S FSZ 2.22222
38 4B52 RDF 2.22222
39 5OFW 9TW 2.22222
40 2ZL4 ALA ALA ALA ALA 2.22222
41 5AZC PGT 2.33333
42 2QZT PLM 2.7027
43 1SQL GUN 2.73973
44 3O01 DXC 2.77778
45 3HBV ALA LYS ALA SER GLN ALA ALA 2.77778
46 4DV8 0LX 2.77778
47 4KX8 L2O VAL VAL ASP 2.77778
48 5N26 CPT 2.77778
49 3WLV AZA 2.77778
50 4UMJ BFQ 2.77778
51 1SBR VIB 2.77778
52 3G4G D71 2.77778
53 5LWY OLB 2.80374
54 2YIP YIO 2.89855
55 5CHR 4NC 2.91971
56 3WV1 WHH 2.92398
57 4RJD TFP 3.0303
58 5TVI MYR 3.26087
59 3Q2H QHF 3.33333
60 2YB9 HA0 3.33333
61 3AQT RCO 3.33333
62 3HP9 CF1 3.33333
63 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 3.33333
64 1C1X HFA 3.33333
65 5V3Y 5V8 3.33333
66 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.33333
67 5O2N FLC 3.33333
68 4F06 PHB 3.33333
69 6AYU MLI 3.33333
70 3ROE THM 3.33333
71 1BW9 PPY 3.33333
72 3T03 3T0 3.33333
73 3ZJX BOG 3.33333
74 5YWX 93C 3.33333
75 5YWX GSH 3.33333
76 1MMQ RRS 3.52941
77 3K1X DBX 3.84615
78 1ZVX FIN 3.88889
79 1KAP GLY SER ASN SER 3.88889
80 2YFB SIN 3.88889
81 2YIV YIV 3.88889
82 3G58 988 3.88889
83 2Z9I GLY ALA THR VAL 3.88889
84 5A9A UTP 3.88889
85 1XMY ROL 3.88889
86 4OEV OXL 3.88889
87 4OIV XX9 3.88889
88 3UCJ AZM 3.88889
89 1XM4 PIL 3.88889
90 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 3.88889
91 4LO6 SIA GAL 3.88889
92 3JU6 ARG 3.88889
93 1XMU ROF 3.88889
94 1B7H LYS NLE LYS 3.88889
95 3N71 SFG 3.88889
96 3TGE TGE 3.88889
97 4O4Z N2O 3.8961
98 2YLD CMO 3.93701
99 3KO0 TFP 3.9604
100 1IDA 0PO 4.0404
101 5H0U HIS HIS HIS HIS HIS HIS 4.11765
102 1DTL BEP 4.34783
103 1YP1 LYS ASN LEU 4.44444
104 4ZW3 4S9 4.44444
105 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 4.44444
106 2W14 WR2 4.44444
107 2XQ0 BES 4.44444
108 2VJ8 HA2 4.44444
109 1Y79 LYS TRP 4.44444
110 5T63 ALA ALA ALA ALA 4.44444
111 3C88 ARG ARG GLY CYS NH2 4.44444
112 5X13 HC4 4.44444
113 3X01 AMP 4.44444
114 4G05 JZ3 4.44444
115 2OUA AES 4.44444
116 5OD2 GLC 4.44444
117 1YKD CMP 4.44444
118 1NAA ABL 4.44444
119 2B56 U5P 4.44444
120 1NAA 6FA 4.44444
121 5EY0 GTP 4.44444
122 1RV1 IMZ 4.70588
123 4GAA BES 5
124 1PNF NDG NAG 5
125 3COW 52H 5
126 5LX9 OLB 5.28169
127 1MID LAP 5.49451
128 5C1M OLC 5.55556
129 4AIG FLX 5.55556
130 3E70 GDP 5.55556
131 5KD8 TNR 5.55556
132 5Y02 HBX 5.55556
133 2XMY CDK 5.55556
134 1TL2 NDG 5.55556
135 5G57 6M5 5.55556
136 2JC9 ADN 5.55556
137 4OYA 1VE 5.55556
138 3LN0 52B 5.55556
139 5FUS DAO 5.55556
140 5HCN DAO 5.55556
141 2WMC MGP 5.61798
142 4WZV E40 5.625
143 6HT0 GQ8 5.80645
144 2V5E SCR 5.94059
145 3LXI CAM 6.11111
146 4BXK 1IU 6.11111
147 4WGF HX2 6.11111
148 1R5L VIV 6.11111
149 6BR8 PGV 6.11111
150 3ENV ABF 6.11111
151 1G8K MGD 6.11111
152 2BHW NEX 6.11111
153 1GJW GLC 6.11111
154 6C0T EE4 6.11111
155 2OWZ CIT 6.11111
156 5G5G MCN 6.11111
157 3W68 VIV 6.11111
158 3W54 RNB 6.11111
159 5MJA 7O3 6.11111
160 1LNX URI 6.17284
161 5YZ2 AMP 6.25
162 1RM8 BAT 6.50888
163 4F4S EFO 6.57895
164 3KP6 SAL 6.62252
165 1FBL HTA 6.66667
166 1R55 097 6.66667
167 6BMN PAP 6.66667
168 6BTN E8M 6.66667
169 5CX6 CDP 6.66667
170 4TMN 0PK 6.66667
171 4E28 9MZ 6.66667
172 2OZ5 7XY 6.66667
173 1BRW URA 6.66667
174 6BR9 PGV 6.66667
175 1OFD FMN 6.66667
176 1OFD AKG 6.66667
177 4WKI 3PW 6.80851
178 5C9J DAO 7.07071
179 2TCL RO4 7.10059
180 5OSW DIU 7.22222
181 4AR8 IP8 GLY PRO ALA 7.22222
182 4URX FK1 7.22222
183 2QCX PF1 7.22222
184 4IGH 1EA 7.22222
185 4IGH ORO 7.22222
186 4IGH FMN 7.22222
187 5Z3I ADE 7.22222
188 1J78 OLA 7.22222
189 1NF8 BOG 7.22222
190 4LHD GLY 7.22222
191 6EGU 43Y 7.22222
192 4IN9 SER TRP PHE PRO 7.22892
193 1Q3P GLU ALA GLN THR ARG LEU 7.33945
194 5V4R MGT 7.40741
195 5X80 SAL 7.5
196 5OM2 DXT 7.5
197 4K90 MLA 7.77778
198 3DWB RDF 7.77778
199 4I90 CHT 7.77778
200 1ZPD CIT 7.77778
201 4UZI IMD 7.77778
202 3CV2 COA 7.77778
203 5BWD FUM 7.77778
204 5IM3 DTP 7.77778
205 2D5X L35 8.21918
206 3GF2 SAL 8.21918
207 2FV5 541 8.33333
208 4QOM PYG 8.33333
209 4C2C ALA ALA ALA 8.33333
210 2Q8G AZX 8.33333
211 5JY4 ISC 8.33333
212 2FN1 PYR 8.33333
213 2J9L ATP 8.33333
214 1KUK PCA LYS TRP 8.37438
215 1Q3A NGH 8.48485
216 1HFS L04 8.75
217 2GWH PCI 8.88889
218 1TE2 PGA 8.88889
219 3R9V DXC 8.88889
220 5ME4 HP4 8.88889
221 4YMX ARG 8.88889
222 5X8G S0N 8.88889
223 5EK3 5PK 8.88889
224 5LOF 70R 8.88889
225 2X1L MET 8.88889
226 6BVM EBV 8.98204
227 6BVK EAV 8.98204
228 6BVJ EAS 8.98204
229 6BVL EBY 8.98204
230 6BVI EC4 8.98204
231 3KPB SAM 9.01639
232 3NFD COA 9.15033
233 3ZVS MLI 9.375
234 4DD8 BAT 9.44444
235 5DCH 1YO 9.44444
236 4IJ6 SEP 9.44444
237 2GBB CIT 9.61539
238 4YV5 SVR 9.83607
239 1ZED PNP 10
240 4MGA 27L 10
241 5AAV GW5 10
242 4TV1 36M 10
243 5OCA 9QZ 10
244 4MG9 27K 10
245 4JJF N2I 10
246 3SFI 3SF 10
247 4XTX 590 10
248 3B9Z CO2 10.5556
249 3AHO 3A2 10.6383
250 1BKC INN 11.1111
251 4CA5 3EF 11.1111
252 5O7E 9NB 11.1111
253 5BSR COA 11.1111
254 5BSR AMP 11.1111
255 3NJQ NJQ 11.1111
256 5EEH P9P 11.1111
257 3I7V B4P 11.194
258 2UZH IPE 11.5152
259 1JGS SAL 11.5942
260 6CB2 OLC 11.6667
261 2YLN CYS 11.6667
262 3AB1 FAD 11.6667
263 5WBF LAC 11.6667
264 2P4Y C03 11.6667
265 3FUR Z12 11.6667
266 3RET PYR 11.8812
267 3RET SAL 11.8812
268 5W7B MYR 12.2222
269 5Z84 CHD 12.9412
270 5ZCO CHD 12.9412
271 5W97 CHD 12.9412
272 6F97 FAD 13.3333
273 2ZXG S23 13.8889
274 2Y69 CHD 14.2857
275 2UW1 GVM 14.4444
276 3CEV ARG 14.4444
277 5KK4 44E 14.5833
278 5ZI7 GLU 15
279 1XVB BHL 15
280 1NU4 MLA 15.4639
281 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 15.5556
282 3OKI OKI 15.5556
283 5KDS A2G THR ALA PRO GLY GLY NAG SIA 16.1111
284 3GUZ PAF 16.4773
285 1BWO LPC 16.6667
286 3X1M COA 16.9811
287 4L8F MTX 17.7778
288 4OGQ 2WD 18.9189
289 4OGQ 7PH 18.9189
290 4OGQ 1O2 18.9189
291 4QHP 32Q 20
292 4UCC ZKW 20.5556
293 4PGK Y69 20.5556
294 6CGN DA 21.6667
295 3SE5 ANP 21.9512
296 1T0S BML 23.2558
297 1PVC ILE SER GLU VAL 23.3333
298 3N7S 3N7 23.4783
299 5M36 9SZ 26.3158
Pocket No.: 2; Query (leader) PDB : 1S17; Ligand: GNR; Similar sites found with APoc: 63
This union binding pocket(no: 2) in the query (biounit: 1s17.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5WHU SIA GAL GLC None
2 5N53 8NB None
3 1N13 AG2 None
4 6FX2 FUC C4W NAG BMA MAN NAG GAL None
5 2QQC AG2 None
6 2P39 SCR 1.29032
7 2BVE PH5 1.68067
8 4RFM 3P6 1.8797
9 3WYJ H78 2.22222
10 2E2R 2OH 2.22222
11 2P0D I3P 2.32558
12 2ED4 FAD 2.68456
13 5UC9 MYR 2.77778
14 5IUY BOG 2.77778
15 1YXM ADE 2.77778
16 6ASZ GLN THR ALA ARG M3L SER 2.89855
17 1C1D PHE 3.33333
18 6C1R EFD 3.33333
19 2V57 PRL 3.33333
20 5CSD ACD 3.77358
21 3QPB URA 3.88889
22 1EJH M7G 3.88889
23 4L3L 5FI 3.88889
24 1QJI PKF 3.88889
25 1M5B BN1 4.44444
26 6BSW UDP 5
27 5OLK DTP 5
28 5AE2 FAD 5
29 2IDV M7G 5.08475
30 5Y02 MXN 5.55556
31 1TV5 A26 6.11111
32 1TV5 N8E 6.11111
33 1V97 MTE 6.11111
34 4JNA FAD 6.11111
35 1XQP 8HG 6.66667
36 1Y7I SAL 6.71642
37 6CHP F0Y 7.45342
38 4J24 EST 7.77778
39 4AF5 CIT 7.77778
40 4J26 EST 7.77778
41 1RZX ACE VAL LYS GLU SER LEU VAL 8.16327
42 4RLT FSE 8.22785
43 5OHJ 9VE 8.88889
44 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 8.88889
45 1H8P PC 9.17431
46 3UG4 AHR 9.44444
47 1LYX PGA 9.44444
48 2QE4 JJ3 10
49 5DXG EST 10
50 5DX3 EST 10
51 5KXE 6Y2 10
52 5HYR EST 10
53 5WGD EST 10
54 3UUD EST 10
55 5WGQ EST 10
56 3G9E RO7 11.6667
57 1OUK 084 12.2222
58 1N8V BDD 12.5
59 3TDC 0EU 12.7778
60 3H0L ADP 13.3333
61 6DQU GLY ILE ILE ASN THR LEU 13.3333
62 2V58 LZJ 18.3333
63 5TCI 79V 22.2222
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