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Receptor
PDB id Resolution Class Description Source Keywords
1G27 2.1 Å EC: 3.5.1.31 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXE INHIBITOR BB-3497 ESCHERICHIA COLI BB-3497 INHIBITION POLYPEPTIDE DEFORMYLASE HYDROLASE
Ref.: ANTIBIOTIC ACTIVITY AND CHARACTERIZATION OF BB-3497 PEPTIDE DEFORMYLASE INHIBITOR. ANTIMICROB.AGENTS CHEMOTHER. V. 45 563 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB1 A:1001;
B:2002;
C:3003;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 7 nM
329.435 C16 H31 N3 O4 CCCC[...
NI A:9001;
B:9002;
C:9003;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1G27 2.1 Å EC: 3.5.1.31 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXE INHIBITOR BB-3497 ESCHERICHIA COLI BB-3497 INHIBITION POLYPEPTIDE DEFORMYLASE HYDROLASE
Ref.: ANTIBIOTIC ACTIVITY AND CHARACTERIZATION OF BB-3497 PEPTIDE DEFORMYLASE INHIBITOR. ANTIMICROB.AGENTS CHEMOTHER. V. 45 563 2001
Members (6)
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
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: BB1; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 BB1 1 1
2 BRR 0.481481 0.696429
3 NFH 0.424242 0.821429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found with APoc: 315
This union binding pocket(no: 1) in the query (biounit: 1g27.bio3) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 5C1M OLC None
3 1UO4 PIH None
4 3KO0 TFP None
5 1RM8 BAT None
6 5NNT DPV None
7 1PNF NDG NAG None
8 2OUA AES None
9 5WBF LAC None
10 2WMC MGP None
11 3NFD COA None
12 1RV1 IMZ None
13 4F4S EFO None
14 3SFI 3SF None
15 1UO5 PIH None
16 4HY1 19X None
17 1BWO LPC None
18 4RC8 STE None
19 5K53 STE None
20 4XMF HSM None
21 2ALG DAO None
22 3KIF GDL None
23 5MWE TCE None
24 1ZEI CRS None
25 5C2N NAG None
26 4B6C B5U None
27 6BOC EU7 None
28 3ZVS MLI 1.25
29 4WKI 3PW 1.2766
30 3I7V B4P 1.49254
31 4AIG FLX 1.78571
32 2YFB SIN 1.78571
33 6BR8 PGV 1.78571
34 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 1.78571
35 1M2Z BOG 1.78571
36 3W68 VIV 1.78571
37 4OIV XX9 1.78571
38 1O8B ABF 1.78571
39 3OKI OKI 1.78571
40 2FP2 TSA 1.80723
41 2GBB CIT 1.92308
42 2VWA PTY 1.9802
43 2ED4 FAD 2.01342
44 5OD2 GLC 2.38095
45 5HCN DAO 2.38095
46 1QJI PKF 2.38095
47 6BR9 PGV 2.38095
48 4XU6 TDA 2.38095
49 3SE5 ANP 2.43902
50 4DS0 A2G GAL NAG FUC 2.45399
51 1SQL GUN 2.73973
52 5LWY OLB 2.97619
53 3B9Z CO2 2.97619
54 1KAP GLY SER ASN SER 2.97619
55 5N26 CPT 2.97619
56 3DWB RDF 2.97619
57 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 2.97619
58 5BSR COA 2.97619
59 5NM7 GLY 2.97619
60 5BSR AMP 2.97619
61 5C9P FUC 2.97619
62 1TL2 NDG 2.97619
63 1P4V GLY 2.97619
64 1RZM E4P 2.97619
65 3CV2 COA 2.97619
66 5UGW GSH 3.57143
67 2W14 WR2 3.57143
68 1TE2 PGA 3.57143
69 5O7E 9NB 3.57143
70 3E70 GDP 3.57143
71 4BXK 1IU 3.57143
72 3AQT RCO 3.57143
73 4LO6 SIA GAL 3.57143
74 1M5B BN1 3.57143
75 3X01 AMP 3.57143
76 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 3.57143
77 2OZ5 7XY 3.57143
78 1Y7I SAL 3.57143
79 1SBR VIB 3.57143
80 4YMX ARG 3.57143
81 5AZC PGT 3.57143
82 1J78 OLA 3.57143
83 5KAU RHQ 3.63636
84 1DTL BEP 3.72671
85 5LX9 OLB 3.87324
86 5C9J DAO 4.0404
87 3WV1 WHH 4.16667
88 4ZW3 4S9 4.16667
89 4AR8 IP8 GLY PRO ALA 4.16667
90 5T63 ALA ALA ALA ALA 4.16667
91 3CHT 4NB 4.16667
92 5KD8 TNR 4.16667
93 5X13 HC4 4.16667
94 5E58 CPZ 4.16667
95 4PGK Y69 4.16667
96 1VRP IOM 4.16667
97 6EGU 43Y 4.16667
98 3CEV ARG 4.16667
99 4OB6 S2T 4.16667
100 3COW 52H 4.16667
101 4RHP PEF 4.16667
102 5IM3 DTP 4.16667
103 1WLJ U5P 4.16667
104 1UAY ADN 4.16667
105 5Y02 HBX 4.6729
106 2GWH PCI 4.7619
107 6BMN PAP 4.7619
108 4MRP GSH 4.7619
109 2Q8G AZX 4.7619
110 1YXM ADE 4.7619
111 3SQP 3J8 4.7619
112 2AX9 BHM 4.7619
113 4WZ8 3W7 4.7619
114 5IUY BOG 4.7619
115 5KDS A2G THR ALA PRO GLY GLY NAG SIA 4.7619
116 3EE4 MYR 4.7619
117 1NAA 6FA 4.7619
118 4URX FK1 4.7619
119 3O7J 2AL 4.7619
120 4UMJ BFQ 4.7619
121 4JJF N2I 4.7619
122 5X40 ACP 4.7619
123 1MJT ITU 4.7619
124 6BVM EBV 4.79042
125 6BVK EAV 4.79042
126 5V4R MGT 4.93827
127 4OGQ 2WD 5
128 4OGQ 1O2 5
129 4OGQ 7PH 5
130 5M36 9SZ 5.35714
131 6F5W KG1 5.35714
132 4QOM PYG 5.35714
133 2CIX CEJ 5.35714
134 2XQ0 BES 5.35714
135 6CS8 F9Y 5.35714
136 5TVI MYR 5.43478
137 1MID LAP 5.49451
138 3X1M COA 5.66038
139 3Q2H QHF 5.95238
140 4CA5 3EF 5.95238
141 1XMY ROL 5.95238
142 4L8F MTX 5.95238
143 4K90 MLA 5.95238
144 2IV2 MGD 5.95238
145 5V3Y 5V8 5.95238
146 1XM4 PIL 5.95238
147 1ZPD CIT 5.95238
148 3B6R CRN 5.95238
149 5FCF GLY GLY GLY 5.95238
150 2JC9 ADN 5.95238
151 1XMU ROF 5.95238
152 5FQK 6NT 5.95238
153 5EEH P9P 5.95238
154 6G33 5ID 5.95238
155 3K1X DBX 6.15385
156 3N7S 3N7 6.25
157 2QZT PLM 6.30631
158 1FBL HTA 6.54762
159 1ATL 0QI 6.54762
160 1MMQ RRS 6.54762
161 2TCL RO4 6.54762
162 1ZED PNP 6.54762
163 2VJ8 HA2 6.54762
164 3G58 988 6.54762
165 5IDM C2E 6.54762
166 4OEV OXL 6.54762
167 1R5L VIV 6.54762
168 4B52 RDF 6.54762
169 3HW5 AMP 6.54762
170 2C78 PUL 6.54762
171 2BVE PH5 6.72269
172 4WZV E40 6.875
173 5X80 SAL 6.875
174 4JX1 CAH 7.07965
175 5W7B MYR 7.0922
176 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 7.14286
177 2Z9I GLY ALA THR VAL 7.14286
178 4MGA 27L 7.14286
179 2V5E SCR 7.14286
180 5EK3 5PK 7.14286
181 2J9L ATP 7.14286
182 3C88 ARG ARG GLY CYS NH2 7.14286
183 6H8S FSZ 7.14286
184 4TV1 36M 7.14286
185 3LXI CAM 7.14286
186 5Z3I ADE 7.14286
187 1NF8 BOG 7.14286
188 4MG9 27K 7.14286
189 1N8V BDD 7.14286
190 3NB0 G6P 7.14286
191 3RMK BML 7.22892
192 1Q3A NGH 7.27273
193 5CHR 4NC 7.29927
194 1LNX URI 7.40741
195 2ZXG S23 7.7381
196 2J83 BAT 7.7381
197 3TDC 0EU 7.7381
198 2YIV YIV 7.7381
199 2UW1 GVM 7.7381
200 1U6R IOM 7.7381
201 2B56 U5P 7.7381
202 5W7D MYR 7.7381
203 5W7D PX8 7.7381
204 2HW1 FRU 7.7381
205 3ROE THM 7.7381
206 3UG4 AHR 7.7381
207 4P8O 883 7.7381
208 5C2H 4XU 7.7381
209 4O4Z N2O 7.79221
210 2YLD CMO 7.87402
211 1JGS SAL 7.97101
212 1HFS L04 8.125
213 3GF2 SAL 8.21918
214 3O01 DXC 8.33333
215 1R6N 434 8.33333
216 5OCA 9QZ 8.33333
217 3ZJX BOG 8.33333
218 2E2R 2OH 8.33333
219 3WLV AZA 8.33333
220 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 8.33333
221 2Y69 CHD 8.57143
222 1ZVX FIN 8.58896
223 3KP6 SAL 8.60927
224 3HBV ALA LYS ALA SER GLN ALA ALA 8.92857
225 4KX8 L2O VAL VAL ASP 8.92857
226 3R9V DXC 8.92857
227 4RFM 3P6 8.92857
228 2R4J 13P 8.92857
229 2R4J FAD 8.92857
230 3LN0 52B 8.92857
231 3WCA FPS 8.92857
232 1UUY PPI 8.98204
233 3RV5 DXC 8.98876
234 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 9.18367
235 1YP1 LYS ASN LEU 9.52381
236 4GAA BES 9.52381
237 4C2C ALA ALA ALA 9.52381
238 3AHO 3A2 9.52381
239 5G5G MCN 9.52381
240 5UC9 MYR 9.52381
241 6F6E PLM 9.52381
242 1G8K MGD 9.52381
243 1MT1 AG2 9.73451
244 5OM2 DXT 10
245 5ZI7 GLU 10.119
246 4C2G ALA ALA ALA ALA 10.119
247 4COL DTP 10.119
248 5G57 6M5 10.119
249 4DV8 0LX 10.7143
250 4QHP 32Q 10.7143
251 4AG8 AXI 10.7143
252 4DD8 BAT 11.3095
253 1KUK PCA LYS TRP 11.3095
254 4UCC ZKW 11.3095
255 4TMN 0PK 11.3095
256 5DUF G7A 11.3095
257 3N75 G4P 11.3095
258 2ZCQ B65 11.3095
259 4WGF HX2 11.9048
260 5YZ2 AMP 11.9048
261 4IGH 1EA 11.9048
262 4IGH ORO 11.9048
263 4IGH FMN 11.9048
264 4Z87 GDP 11.9048
265 1UUO BRF 11.9048
266 5JY4 ISC 11.9048
267 3KV8 FAH 12.2302
268 3V1S 0LH 12.5
269 5Z84 CHD 13.0435
270 5ZCO CHD 13.0435
271 5W97 CHD 13.0435
272 5ZCO PEK 13.0435
273 5OSW DIU 13.0952
274 4V3I ASP LEU THR ARG PRO 13.0952
275 1T0S BML 13.0952
276 2FN1 PYR 13.0952
277 1W6F ISZ 13.0952
278 4IN9 SER TRP PHE PRO 13.253
279 4RYV ZEA 13.5484
280 2YB9 HA0 13.6905
281 4XNV BUR 13.6905
282 1XVB BHL 13.6905
283 1XVB 3BR 13.6905
284 2V57 PRL 13.6905
285 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 15.2381
286 6CGN DA 15.4762
287 1BKC INN 16.6667
288 2FV5 541 16.6667
289 6BTN E8M 16.6667
290 3HP9 CF1 16.6667
291 2V3V MGD 16.6667
292 5CX6 CDP 17.2619
293 2P4Y C03 17.2619
294 3H0A D30 17.2619
295 4F06 PHB 18.4524
296 1OUK 084 19.0476
297 1N13 AG2 19.469
298 2QQD AG2 19.6429
299 2QQC AG2 19.6429
300 1T36 ORN 19.6429
301 1R55 097 20.2381
302 4E28 9MZ 20.2381
303 1Y79 LYS TRP 20.8333
304 3H0L ADP 23.2143
305 2X0K PPV 25
306 4RJD TFP 27.2727
307 6MVU K4V 27.381
308 5JF2 SF7 38.0952
309 4EOX 0S5 38.6905
310 1Q1Y BB2 38.6905
311 3G6N MET ALA SER 38.6905
312 2OKL BB2 42.2619
313 5MTE BB2 44.5255
314 3G5K BB2 47.619
315 1LQY BB2 47.619
Pocket No.: 2; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found with APoc: 54
This union binding pocket(no: 2) in the query (biounit: 1g27.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3KIH GDL None
2 2IDV M7G 1.78571
3 4HZ0 1AV 1.78571
4 1TO9 HMH 2.38095
5 3AKI AH8 2.38095
6 1O9W NAG 2.97619
7 1W0H AMP 2.97619
8 1V97 MTE 2.97619
9 5K52 OCD 3.57143
10 1UY4 XYP XYP XYP XYP 4.13793
11 3WYJ H78 4.16667
12 3V78 ET 4.16667
13 5LGA 6VH 4.16667
14 1EJ4 M7G 4.16667
15 1LYX PGA 4.7619
16 1XF1 CIT 4.7619
17 5CSD ACD 5.03145
18 3KDU NKS 5.35714
19 3AYI FAD 5.35714
20 3AYI HCI 5.35714
21 1VLH PNS 5.35714
22 3KFC 61X 5.35714
23 2OBD PCW 5.35714
24 2P0D I3P 5.42636
25 4ORM ORO 5.95238
26 4ORM FMN 5.95238
27 4ORM 2V6 5.95238
28 3OBT SLB 5.95238
29 5OHJ 9VE 5.95238
30 1TV5 A26 5.95238
31 5VKM GAL SIA 5.95238
32 2D5X L35 6.16438
33 3G4G D71 6.54762
34 6DQU GLY ILE ILE ASN THR LEU 6.54762
35 3KPB SAM 6.55738
36 5AAV GW5 7.14286
37 3TGE TGE 7.14286
38 1J1R ADE 7.7381
39 5HI5 63Q 8.33333
40 4NAT ADP 10
41 4GDX GLU 10.7143
42 3RET SAL 10.8911
43 3RET PYR 10.8911
44 1PVC ILE SER GLU VAL 11.3095
45 4WVH ASP HIS ASP ALA HIS ALA 11.9048
46 4JNA FAD 11.9048
47 5FVJ ACO 12.6506
48 1TT8 PHB 13.4146
49 2VQD AP2 13.6905
50 6BYM HC3 14.881
51 5ME4 HP4 15.6934
52 2HFP NSI 17.2619
53 3T03 3T0 17.2619
54 3FUR Z12 17.2619
Pocket No.: 3; Query (leader) PDB : 1G27; Ligand: BB1; Similar sites found with APoc: 36
This union binding pocket(no: 3) in the query (biounit: 1g27.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5KK4 44E None
2 6BOC RIM None
3 5H0U HIS HIS HIS HIS HIS HIS 1.78571
4 4CZG ADP 3.57143
5 4P6G 2FZ 3.57143
6 1AOE GW3 4.16667
7 1AOE NDP 4.16667
8 1XOC VAL ASP SER LYS ASN THR SER SER TRP 4.16667
9 1EJH M7G 4.16667
10 1B7H LYS NLE LYS 4.16667
11 3K0T BGC 4.1958
12 2JGV ADP 4.7619
13 1HSR BHO 4.7619
14 2HIM ASN 4.7619
15 2P3V SRT 5.35714
16 1VAY AZA 5.95238
17 1C3X 8IG 5.95238
18 3KC1 2T6 5.95238
19 1VL1 CIT 6.46552
20 4IJ6 SEP 6.54762
21 1C1X HFA 6.54762
22 2NV2 GLN 7.7381
23 4BAE RWX 7.7381
24 5Y6Q FAD 8.33333
25 4YDD MGD 8.92857
26 4YDD MD1 8.92857
27 5FUS DAO 8.92857
28 4NOS H4B 9.52381
29 3RS8 ALA TRP LEU PHE GLU ALA 9.52381
30 6HT0 GQ8 9.67742
31 4MN3 ACE PHE ALA TYR M3L SER NH2 10.7143
32 3AB1 FAD 11.3095
33 3ENV ABF 11.9048
34 1UUO ORO 11.9048
35 1UUO FMN 11.9048
36 2WE0 UMP 11.9048
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