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Receptor
PDB id Resolution Class Description Source Keywords
4DR9 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCU ELONGATUS IN COMPLEX WITH ACTINONIN SYNECHOCOCCUS ELONGATUS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND FUNCTION OF A CYANOPHAGE-ENCODED PEPT DEFORMYLASE. ISME J V. 7 1150 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN C:201;
B:201;
D:201;
A:201;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
BB2 B:203;
C:204;
D:203;
A:203;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 10 nM
385.498 C19 H35 N3 O5 CCCCC...
BR C:203;
D:202;
B:202;
C:202;
A:202;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DR9 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCU ELONGATUS IN COMPLEX WITH ACTINONIN SYNECHOCOCCUS ELONGATUS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND FUNCTION OF A CYANOPHAGE-ENCODED PEPT DEFORMYLASE. ISME J V. 7 1150 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4DR9 ic50 = 10 nM 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: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found with APoc: 291
This union binding pocket(no: 1) in the query (biounit: 4dr9.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1Q3A NGH None
2 1UO4 PIH None
3 5NNT DPV None
4 1UO5 PIH None
5 4V3I ASP LEU THR ARG PRO None
6 1MID LAP None
7 2OUA AES None
8 6F5W KG1 None
9 3SE5 ANP None
10 4WG0 CHD None
11 1UY4 XYP XYP XYP XYP None
12 5X80 SAL None
13 3OKI OKI 1.04167
14 5AZC PGT 1.04167
15 3WV1 WHH 1.16959
16 4DV8 0LX 1.5625
17 3R9V DXC 1.5625
18 3PE2 E1B 1.5625
19 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 1.5625
20 2P4Y C03 1.5625
21 5A0R ACE GLU VAL ASN PRO 1.5625
22 6C1R EFD 1.5625
23 5UGW GSH 1.71429
24 1MT1 AG2 1.76991
25 3X1M COA 1.88679
26 3SQP 3J8 2.08333
27 4XU6 TDA 2.08333
28 3SP6 IL2 2.08333
29 1UUY PPI 2.39521
30 1ATL 0QI 2.60417
31 4AIG FLX 2.60417
32 4AR8 IP8 GLY PRO ALA 2.60417
33 4CA5 3EF 2.60417
34 2YB9 HA0 2.60417
35 6BR8 PGV 2.60417
36 5V3Y 5V8 2.60417
37 4B52 RDF 2.60417
38 4H6Q TFB 2.60417
39 4RHP PEF 2.60417
40 3WYJ H78 2.60417
41 2BHW NEX 2.60417
42 5IJJ I6P 2.60417
43 5N5U 7N8 2.60417
44 2D5Z L35 2.73973
45 5V4R MGT 3.08642
46 1NU4 MLA 3.09278
47 3O01 DXC 3.125
48 2ZXG S23 3.125
49 5O7E 9NB 3.125
50 4WZV E40 3.125
51 6MVU K4V 3.125
52 3V1S 0LH 3.125
53 1ZPD CIT 3.125
54 3D3X ARG ILE MET GLU NH2 3.125
55 5IUY BOG 3.125
56 4A7W GTP 3.125
57 4URX FK1 3.125
58 4ZCC FAD 3.125
59 4ZCC NAI 3.125
60 4QED NAP 3.125
61 5WJ6 B4A 3.125
62 3VOZ 04A 3.125
63 3TCT 3MI 3.14961
64 1N8V BDD 3.57143
65 5FVJ ACO 3.61446
66 2YIP YIO 3.62319
67 2GWH PCI 3.64583
68 4DD8 BAT 3.64583
69 1R6N 434 3.64583
70 1ZED PNP 3.64583
71 2YFB SIN 3.64583
72 5OSW DIU 3.64583
73 4MRP GSH 3.64583
74 2Z9I GLY ALA THR VAL 3.64583
75 4PGK Y69 3.64583
76 5KD8 TNR 3.64583
77 4WGF HX2 3.64583
78 5DCH 1YO 3.64583
79 5FUS DAO 3.64583
80 6ARJ SAH 3.64583
81 3GKJ HC3 3.64583
82 5Z3I ADE 3.64583
83 1ZVX FIN 3.68098
84 1HFS L04 3.75
85 2ED4 FAD 4.02685
86 3GF2 SAL 4.10959
87 2W14 WR2 4.16667
88 1R55 097 4.16667
89 1KAP GLY SER ASN SER 4.16667
90 3E70 GDP 4.16667
91 3TDC 0EU 4.16667
92 4RW3 TDA 4.16667
93 3H0A D30 4.16667
94 3LXI CAM 4.16667
95 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 4.16667
96 1B7H LYS NLE LYS 4.16667
97 3ZJX BOG 4.16667
98 1R5L VIV 4.16667
99 3COW 52H 4.16667
100 5C1M OLC 4.16667
101 5NJI 8Z2 4.16667
102 5KDS A2G THR ALA PRO GLY GLY NAG SIA 4.16667
103 3GD8 GOL 4.16667
104 4JJF N2I 4.16667
105 4RW3 PLM 4.16667
106 3W68 VIV 4.16667
107 5OD2 GLC 4.16667
108 4COL DTP 4.16667
109 4IN9 SER TRP PHE PRO 4.21687
110 5TVI O8N 4.34783
111 5CHR 4NC 4.37956
112 5N26 CPT 4.3956
113 3NFD COA 4.57516
114 3Q2H QHF 4.6875
115 2J83 BAT 4.6875
116 3HBV ALA LYS ALA SER GLN ALA ALA 4.6875
117 4KX8 L2O VAL VAL ASP 4.6875
118 4GAA BES 4.6875
119 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.6875
120 4LO6 SIA GAL 4.6875
121 3H0L ADP 4.6875
122 5G57 6M5 4.6875
123 1YKD CMP 4.6875
124 1XVB BHL 4.6875
125 4Z87 GDP 4.6875
126 1XMY ROL 4.77387
127 1XM4 PIL 4.77387
128 1XMU ROF 4.77387
129 6CHP F0Y 4.96894
130 3ZVS MLI 5
131 1VLH PNS 5.20231
132 1YP1 LYS ASN LEU 5.20833
133 5ZI7 GLU 5.20833
134 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 5.20833
135 3AQT RCO 5.20833
136 2XQ0 BES 5.20833
137 4TMN 0PK 5.20833
138 1OUK 084 5.20833
139 3C88 ARG ARG GLY CYS NH2 5.20833
140 2RCU BUJ 5.20833
141 3NB0 G6P 5.20833
142 5UC9 MYR 5.20833
143 5C2H 4XU 5.20833
144 5C2H 4PX 5.20833
145 1MMQ RRS 5.29412
146 1DTL BEP 5.59006
147 3B9Z CO2 5.72917
148 2YIV YIV 5.72917
149 6BMN PAP 5.72917
150 4ORM ORO 5.72917
151 4ORM FMN 5.72917
152 4ORM 2V6 5.72917
153 2JC9 ADN 5.72917
154 5O2N FLC 5.72917
155 6DWI HD4 5.72917
156 4RC8 STE 5.72917
157 3KPB SAM 5.7377
158 2V57 PRL 5.78947
159 1JGS SAL 5.7971
160 3KO0 TFP 5.94059
161 3I7V B4P 5.97015
162 3LDW ZOL 6.06061
163 5LX9 OLB 6.25
164 1GEG GLC 6.25
165 3G58 988 6.25
166 5CX6 CDP 6.25
167 1XON PIL 6.25
168 1Q7E MET 6.25
169 6F97 FAD 6.25
170 3G4G D71 6.25
171 1XOC VAL ASP SER LYS ASN THR SER SER TRP 6.25
172 3GWT 066 6.25
173 5CSD ACD 6.28931
174 3KP6 SAL 6.62252
175 1BKC INN 6.77083
176 4ZW3 4S9 6.77083
177 2FV5 541 6.77083
178 3UG4 AHR 6.77083
179 4UCC ZKW 6.77083
180 5EK3 5PK 6.77083
181 1B4N GUA 6.77083
182 3HP9 CF1 6.77083
183 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 6.77083
184 2OZ5 7XY 6.77083
185 1NF8 BOG 6.77083
186 5EEH P9P 6.77083
187 4NAT ADP 6.875
188 2YLD CMO 7.08661
189 1RM8 BAT 7.10059
190 4OGQ 2WD 7.29167
191 4OGQ 7PH 7.29167
192 6DQU GLY ILE ILE ASN THR LEU 7.29167
193 3CV2 COA 7.29167
194 4QHP 32Q 7.29167
195 4YDD MGD 7.29167
196 4YDD MD1 7.29167
197 4LY9 S6P 7.29167
198 4LY9 1YY 7.29167
199 4OGQ 1O2 7.29167
200 5HCN DAO 7.29167
201 4OGQ UMQ 7.29167
202 1BWO LPC 7.77778
203 2V3V MGD 7.8125
204 3KH5 AMP 7.8125
205 3KH5 ADP 7.8125
206 1J78 OLA 7.8125
207 3QFA FAD 7.8125
208 4F4S EFO 7.89474
209 2VWA PTY 7.92079
210 5W7B MYR 8.33333
211 1D6Z HY1 8.33333
212 3LN0 52B 8.33333
213 4F06 PHB 8.33333
214 5OLK DTP 8.33333
215 3WCA FPS 8.76712
216 4BXK 1IU 8.85417
217 2IV2 MGD 8.85417
218 4RFM 3P6 8.85417
219 5Y02 HBX 9.34579
220 1FBL HTA 9.375
221 5AAV GW5 9.375
222 4TV1 36M 9.375
223 5NM7 GLY 9.375
224 4MGA 27L 9.375
225 5LKT BCO 9.375
226 1ZEI CRS 9.43396
227 5YZ2 AMP 9.72222
228 1Y79 LYS TRP 9.89583
229 5OHJ 9VE 9.89583
230 3DWB RDF 9.89583
231 2V5E SCR 9.90099
232 2TCL RO4 10.0592
233 2D5X L35 10.274
234 4F8L AES 10.3448
235 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 10.4167
236 3AHO 3A2 10.4167
237 6F6E PLM 10.4167
238 4IGH FMN 10.4167
239 4IGH 1EA 10.4167
240 4IGH ORO 10.4167
241 1IXI 2HP 10.4167
242 5K53 STE 10.4167
243 2FP2 TSA 10.8434
244 2BCG GER 10.9375
245 4UBS DIF 10.9375
246 5LWY OLB 11.215
247 1KUK PCA LYS TRP 11.4583
248 2GBB CIT 11.5385
249 4G86 BNT 11.9792
250 5T63 ALA ALA ALA ALA 11.9792
251 6BTN E8M 11.9792
252 3KXC PLM 12.0253
253 4RJD TFP 12.1212
254 4WZ8 3W7 12.5
255 5K52 OCD 12.5
256 4K90 MLA 12.5
257 4WKI 3PW 13.0208
258 2B56 U5P 13.0208
259 5MT9 SRO 13.3333
260 5XWV 8H6 13.5417
261 2FN1 PYR 14.0625
262 5IM3 DTP 14.0625
263 1M2Z BOG 14.5833
264 3N7S 3N7 14.5833
265 5A4W QCT 14.5833
266 5OCA 9QZ 15.1042
267 1VAY AZA 15.625
268 5M36 9SZ 15.7895
269 2Q8G AZX 16.1458
270 2J9L ATP 16.6667
271 2QZT PLM 17.1171
272 5C9J DAO 17.1717
273 2VJ8 HA2 17.1875
274 6ER9 FAD 17.7083
275 1OFD AKG 18.2292
276 1OFD FMN 18.2292
277 1T0S BML 18.6047
278 2WOR 2AN 19
279 3W54 RNB 20.3125
280 2Y69 CHD 20.6349
281 1N13 AG2 21.2389
282 3EE4 MYR 21.3542
283 2QQC AG2 21.4286
284 2OBD PCW 22.3958
285 5MWE TCE 24.6914
286 5Z84 CHD 27.6596
287 5ZCO CHD 27.6596
288 5W97 CHD 27.6596
289 6BOC EU7 37.037
290 6BOC RIM 37.037
291 5MTE BB2 47.4453
Pocket No.: 2; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found with APoc: 95
This union binding pocket(no: 2) in the query (biounit: 4dr9.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2WMC MGP None
2 1TL2 NDG None
3 2ALG HP6 None
4 2ALG DAO None
5 3WLV AZA 1.04167
6 3K3G MMU 1.5625
7 2HFP NSI 1.5625
8 3T03 3T0 1.5625
9 4XMF HSM 1.63043
10 6BVM EBV 2.08333
11 6BVK EAV 2.08333
12 6BVJ EAS 2.08333
13 4JNA FAD 2.08333
14 6BVL EBY 2.08333
15 6BVI EC4 2.08333
16 2CHT TSA 2.3622
17 4UP4 NAG 2.60417
18 4UP4 NDG 2.60417
19 5AE2 FYC 3.125
20 5TWB FAD 3.125
21 5A9A UTP 3.125
22 1COY FAD 3.125
23 6BWL NAD 3.125
24 5TCI 79V 3.125
25 1SQL GUN 3.42466
26 2OWZ CIT 3.64583
27 1RZM E4P 3.64583
28 5NWI TYR PHE SER SEP ASN 3.64583
29 3D04 SAK 3.77358
30 2UW1 GVM 4.16667
31 3NYQ MCA 4.16667
32 3NYQ AMP 4.16667
33 6AYU MLI 4.16667
34 1SBR VIB 4.16667
35 1EJ4 M7G 4.21053
36 2Y7P SAL 4.6875
37 4O4Z N2O 5.19481
38 1TE2 PGA 5.20833
39 2V58 LZJ 5.20833
40 4YMX ARG 5.20833
41 4OYA 1VE 5.20833
42 4X7R UDP 5.20833
43 4X7R 3YW 5.20833
44 4X7R NTO 5.20833
45 2QA1 FAD 5.20833
46 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.43933
47 2UZH IPE 5.45455
48 3GZ9 D32 5.72917
49 4P6G 2FZ 5.72917
50 1GJW GLC 5.72917
51 3KFC 61X 5.72917
52 6A0S NDP 6.25
53 4CZG QH3 6.25
54 2GJN NIS 6.25
55 1UVC STE 6.59341
56 5LGA 6VH 6.77083
57 5JY4 ISC 6.77083
58 3HW5 AMP 6.77083
59 5BVE 4VG 7.29167
60 3KIF GDL 7.54717
61 3BAZ NAP 7.8125
62 4PYW ACE THR THR ALA ILE NH2 7.8125
63 3KV8 FAH 7.91367
64 5X8G S0N 8.33333
65 3RMK BML 8.43373
66 1H0H MGD 8.85417
67 2P0D I3P 9.30233
68 5WBF LAC 9.375
69 3V78 ET 9.375
70 6BYM HC3 9.375
71 1EZV SMA 9.45946
72 4C2C ALA ALA ALA 9.89583
73 1YXM ADE 9.89583
74 5H0U HIS HIS HIS HIS HIS HIS 10
75 1C3X 8IG 10.4167
76 5KK4 44E 10.4167
77 3KDU NKS 10.9375
78 5LWY OLA 11.215
79 2ZCQ B65 11.4583
80 1FEC FAD 11.9792
81 5C9P FUC 11.9792
82 2C78 PUL 15.1042
83 3R1V AZB 16.5354
84 4WO4 JLS 17
85 2QQD AG2 21.4286
86 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 22.8571
87 5ZCO PGV 27.6596
88 5Z84 PGV 27.6596
89 2DYS PGV 27.6596
90 2DYR PGV 27.6596
91 5ZCO PEK 27.6596
92 5BSR AMP 28.125
93 5BSR COA 28.125
94 6BKK 308 37.037
95 6BKL RIM 37.037
Pocket No.: 3; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found with APoc: 59
This union binding pocket(no: 3) in the query (biounit: 4dr9.bio4) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4IDC 1XX None
2 4IDC NDP None
3 1J1R ADE 1.04167
4 3G9E RO7 1.5625
5 6D6L FY4 1.76471
6 2BIF BOG 2.08333
7 3SFI 3SF 2.08333
8 2NPA MMB 2.08333
9 4Q5M ROC 2.08333
10 5J5R 6G1 2.08333
11 5J5R IMP 2.08333
12 2E2R 2OH 2.08333
13 3X01 AMP 2.29008
14 5UFS 1TA 2.60417
15 2HW2 RFP 2.7972
16 2A1L PCW 3.125
17 1YOK P6L 3.125
18 1RV1 IMZ 3.52941
19 4E5N NAD 3.64583
20 6ESN BWE 3.64583
21 4QOM PYG 3.64583
22 5UWA 8ND 4.16667
23 5MW4 5JU 4.16667
24 3NRZ HPA 4.26829
25 5TVI MYR 4.34783
26 4P6X HCY 5.20833
27 3ENV ABF 5.20833
28 1LLF F23 5.20833
29 4YSX FAD 5.20833
30 1EM6 CP4 5.72917
31 3IPQ 965 5.72917
32 6H8S FSZ 6.25
33 2XCG XCG 6.25
34 4ZGM 32M 6.55738
35 6BA2 7KM 6.77083
36 3TGE TGE 6.77083
37 3EWC MCF 7.29167
38 2I0G I0G 7.8125
39 3U3U EAH 7.8125
40 2RHQ GAX 8.33333
41 4QWT ACD 8.33333
42 4YJK URA 8.85417
43 1VA6 P2S 9.375
44 1VA6 ADP 9.375
45 2QE4 JJ3 9.375
46 1SR7 MOF 10.4167
47 3CXH SMA 10.7143
48 5U3F 7TS 10.9375
49 1XL8 OCB 11.4583
50 4WBD CIT 13.5417
51 2O4N TPV 14.1414
52 3T3C 017 14.1414
53 5OJ7 AR6 15.1042
54 2P3C 3TL 16.1616
55 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 17
56 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 17.3469
57 4NTC FAD 19.7917
58 3QUZ QUV 21.2121
59 3RUG DB6 21.2121
Pocket No.: 4; Query (leader) PDB : 4DR9; Ligand: BB2; Similar sites found with APoc: 30
This union binding pocket(no: 4) in the query (biounit: 4dr9.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3KC1 2T6 None
2 2FKW RG1 None
3 2JEN GLC GLC XYS XYS 1.5625
4 3FUR Z12 1.5625
5 4ZVI 4S4 2.60417
6 5YWX 93C 2.60417
7 5YWX GSH 2.60417
8 1COY AND 3.125
9 1QJI PKF 3.125
10 1HSR BHO 4.16667
11 5ZRR 9J3 4.16667
12 1XVB 3BR 4.6875
13 2B96 ANN 4.87805
14 2J8C SPO 5.20833
15 2J8C U10 5.20833
16 4B6C B5U 5.20833
17 5X13 HC4 5.31915
18 1FIQ SAL 6.25
19 6FFI D8B 6.25
20 5LOF 70R 6.25
21 2AX9 BHM 6.25
22 5EEH SAH 6.77083
23 5DUF G7A 7.29167
24 1P0F NAP 7.29167
25 5J60 FAD 7.8125
26 1GPE FAD 7.8125
27 2X5W K2B 9.89583
28 5G3N X28 10.2362
29 3HUJ AGH 17.1717
30 2ZWA SAH 18.2292
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