-->
Receptor
PDB id Resolution Class Description Source Keywords
2Z7I 2.1 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPL INHIBITOR BPH-742 SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE GERANYLGERANYL PYROPHOSPHATE BISPHOSPHONCAROTENOID BIOSYNTHESIS ISOPRENE BIOSYNTHESIS MULTIFUNCTIENZYME PROTEIN TRANSPORT TRANSPORT TRANSFERASE TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE B BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATION INVESTIGATION J.MED.CHEM. V. 51 5594 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
742 A:1302;
B:1303;
Valid;
Valid;
none;
none;
ic50 = 0.1 uM
419.391 C16 H38 O6 P3 CCCCC...
MG A:1301;
B:1302;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Z7I 2.1 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPL INHIBITOR BPH-742 SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE GERANYLGERANYL PYROPHOSPHATE BISPHOSPHONCAROTENOID BIOSYNTHESIS ISOPRENE BIOSYNTHESIS MULTIFUNCTIENZYME PROTEIN TRANSPORT TRANSPORT TRANSFERASE TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE B BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATION INVESTIGATION J.MED.CHEM. V. 51 5594 2008
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.2 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 742; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 742 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Z7I; Ligand: 742; Similar sites found with APoc: 83
This union binding pocket(no: 1) in the query (biounit: 2z7i.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5ET3 60C None
2 4MRP GSH 1.76471
3 5UV1 0FV 2.35294
4 3ZGE ASP 2.35294
5 3TL1 JRO 2.51572
6 1Q7E MET 2.64706
7 1MO9 FAD 2.64706
8 1MO9 KPC 2.64706
9 2WTX UDP 2.64706
10 3AI3 SOE 2.6616
11 6CB2 OLC 2.73038
12 4WGF HX2 2.92683
13 2HZL PYR 2.94118
14 3WCA FPS 2.94118
15 3KO0 TFP 2.9703
16 4RHP PEF 2.97872
17 3R9C ECL 3.23529
18 1Q19 SSC 3.23529
19 2Q8G AZX 3.23529
20 1NF8 BOG 3.38164
21 2OZ5 7XY 3.71622
22 2AEL SAZ 3.82353
23 5XJD 87L 4.09091
24 5FPN KYD 4.11765
25 3SDV 911 4.41176
26 1PZO CBT 4.56274
27 5OLK DTP 4.70588
28 3O01 DXC 4.87013
29 1UI0 URA 4.87805
30 5IKH 6BW 5
31 1L0I PSR 5.12821
32 1CZA ADP 5.58824
33 3RV5 DXC 5.61798
34 2YFB SIN 5.81395
35 4QO5 NAG 5.88235
36 3HP9 CF1 5.88235
37 3ECN IBM 5.91716
38 2A1L PCW 5.92593
39 2ZCQ B65 6.14334
40 4LOC OXM 6.17647
41 4UCC ZKW 7.29614
42 4OKZ 3E9 7.35294
43 5B0I BOG 7.64706
44 5CKS GAL 7.94118
45 5LX9 OLB 8.14332
46 5Y02 MXN 8.41121
47 5MWE TCE 8.57143
48 5V4R MGT 8.64198
49 1UO4 PIH 8.82353
50 5C1M OLC 9.45946
51 1LNX URI 9.87654
52 1T0S BML 10.4651
53 4DXJ 0M9 10.5882
54 4DXJ IPE 10.5882
55 3KP6 SAL 10.596
56 2P1C GG3 10.8824
57 1DTL BEP 11.1801
58 4K10 NI9 12.0588
59 4JZB P2H 12.0588
60 4JZX 476 12.0588
61 4JZX IPE 12.0588
62 4JZB IPE 12.0588
63 1N8V BDD 12.5
64 6GMN F4E 14.433
65 1YHM AHD 21.4706
66 2Y69 CHD 22.4852
67 5Z84 CHD 25.8503
68 5W97 CHD 25.8503
69 5ZCO CHD 25.8503
70 5ZCO PGV 25.8503
71 5Z84 PGV 25.8503
72 6B04 C6J 27.3529
73 1UBY DMA 27.9412
74 4LPG 1MV 30.5882
75 3LDW ZOL 31.7647
76 3LDW IPE 31.7647
77 3KRO IPE 33.5593
78 3KRO DST 33.5593
79 3KRO PPV 33.5593
80 3WJO IPE 35.0148
81 4UMJ BFQ 38.5135
82 2O1O RIS 39.1176
83 1RQJ RIS 39.7993
Pocket No.: 2; Query (leader) PDB : 2Z7I; Ligand: 742; Similar sites found with APoc: 300
This union binding pocket(no: 2) in the query (biounit: 2z7i.bio1) has 65 residues
No: Leader PDB Ligand Sequence Similarity
1 4NC7 I3C None
2 4WG0 CHD None
3 6B21 C9V 1.17647
4 5MBC FMN 1.17647
5 2JHP GUN 1.47059
6 1G0C CBI 1.47059
7 4W4S B29 1.66667
8 4D3S BOG 1.70648
9 2HHP FLC 1.76471
10 5WAN FMN 1.76471
11 5GQX GLC GLC GLC GLC GLC GLC GLC 1.76471
12 1I0B PEL 1.80723
13 5EY0 GTP 1.82482
14 5HCN DAO 1.91571
15 5AZC PGT 2
16 3AQT RCO 2.04082
17 5KD8 TNR 2.05882
18 6DIO CIT 2.05882
19 4HDK 13X 2.05882
20 3ETG GWD 2.05882
21 3W54 RNB 2.12766
22 6FK6 DOK 2.14067
23 5UC9 MYR 2.21239
24 3WQM B29 2.32558
25 5IUY BOG 2.35294
26 6FFI D8B 2.35294
27 1XQD DND 2.35294
28 3H4L ANP 2.35294
29 4COL DTP 2.35294
30 2UW1 GVM 2.36686
31 5V3Y 5V8 2.44755
32 2E2R 2OH 2.45902
33 5CXI 5TW 2.46305
34 2NUN ADP 2.47678
35 4O4Z N2O 2.5974
36 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 2.63158
37 3ROE THM 2.64151
38 4J6C STR 2.64706
39 2OBM ADP 2.64706
40 1N20 3AG 2.64706
41 1YKD CMP 2.64706
42 5GUE GGS 2.71903
43 4WUJ FMN 2.72109
44 5URY PAM 2.73973
45 2BCG GER 2.91262
46 3FWN 6PG 2.91667
47 1ZGA HMK 2.94118
48 6AP8 BNY 2.97398
49 5NM7 GLY 3.00752
50 3FAL REA 3.00752
51 2OHV NHL 3.0303
52 5DXE EST 3.06513
53 5WGD EST 3.06513
54 5WGQ EST 3.06513
55 2QA8 GEN 3.10078
56 5HYR EST 3.10078
57 2QZO KN1 3.10078
58 4V3I ASP LEU THR ARG PRO 3.11284
59 4MGA 27L 3.13725
60 4MGB XDH 3.13725
61 4TUZ 36J 3.13725
62 4MGD 27N 3.13725
63 4MG7 27H 3.13725
64 4MG8 27J 3.13725
65 4G86 BNT 3.16901
66 2BJ4 OHT 3.1746
67 5AAV GW5 3.1746
68 4KWD JF2 3.18471
69 4TV1 36M 3.18725
70 3RS8 ALA TRP LEU PHE GLU ALA 3.18725
71 3UUD EST 3.18725
72 3TDC 0EU 3.23529
73 1ZED PNP 3.23529
74 1SJD NPG 3.23529
75 4IA6 EIC 3.23529
76 3V1V GST 3.23529
77 6CIB ADP 3.23529
78 2XN5 FUN 3.23529
79 4U0S ADP 3.23529
80 1GNI OLA 3.23529
81 2WPX ACO 3.24484
82 2ALG DAO 3.26087
83 2WKQ FMN 3.31325
84 3N7S 3N7 3.47826
85 4YUS FMN 3.52941
86 5OSW DIU 3.52941
87 6BMS PLM 3.52941
88 1HK8 DGT 3.52941
89 3V66 D3A 3.52941
90 3MDV CL6 3.52941
91 4OIV XX9 3.53982
92 1POC GEL 3.73134
93 2VOH CIT 3.82166
94 1ZPD CIT 3.82353
95 2O1V ADP 3.82353
96 6BR9 6OU 3.82353
97 5VEQ PMP 3.82353
98 1UOU CMU 3.82353
99 5M77 7K2 7K3 3.82353
100 3B6C SDN 3.84615
101 2WG9 OCA 3.84615
102 1GEG GLC 3.90625
103 5G3N X28 3.93701
104 4F4S EFO 3.94737
105 2VWA PTY 3.9604
106 3KYQ DPV 4.0201
107 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.08163
108 2PX6 DH9 4.11392
109 1S8G DAO 4.13223
110 4DOL PLM 4.14747
111 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 4.20168
112 6A56 LAT 4.26829
113 5X3R 7Y3 4.39024
114 5CX6 CDP 4.41176
115 3FIU POP 4.41767
116 3QKD HI0 4.41989
117 4URN NOV 4.44444
118 3ZCB ATP 4.54545
119 4RJD TFP 4.54545
120 4TQ3 GPP 4.62046
121 1XMY ROL 4.70588
122 3G58 988 4.70588
123 1XM4 PIL 4.70588
124 1XMU ROF 4.70588
125 2YLD CMO 4.72441
126 1R6N 434 4.73934
127 6BR8 6OU 4.7619
128 6BR8 PGV 4.7619
129 2V0U FMN 4.79452
130 5EFW FMN 4.82759
131 5B4B LP5 4.83871
132 4V2O CLQ 4.87805
133 5Z3I ADE 4.90566
134 1KUK PCA LYS TRP 4.92611
135 6GG9 FMN 4.93827
136 6BT4 KPM 4.9505
137 1TV5 N8E 4.96614
138 5W7B MYR 5
139 5ZKC 3C0 5
140 3KB9 BTM 5
141 3S0E EOL 5.04202
142 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 5.05051
143 1LEK GLU GLN TYR LYS PHE TYR SER VAL 5.05051
144 2UXI G50 5.2381
145 3FEI CTM 5.24345
146 6CGN DA 5.29412
147 5FJJ MAN 5.29412
148 2PR5 FMN 5.30303
149 3LLI FAD 5.36398
150 3BPX SAL 5.40541
151 1TMX HGX 5.46075
152 4AIG FLX 5.47264
153 1N9L FMN 5.50459
154 1Y4Z PCI 5.58824
155 3GFZ FMN 5.58824
156 2IYG FMN 5.64516
157 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 5.65217
158 2WNF CG3 A2G GAL 5.7047
159 5UGW GSH 5.71429
160 1YRX FMN 5.78512
161 5HCV 60R 5.83658
162 6C1R EFD 5.88235
163 1XVB 3BR 5.88235
164 5AHO TLA 5.95238
165 6H8S FSZ 5.98007
166 2WOR 2AN 6
167 5E5U MLI 6.03015
168 3Q2H QHF 6.06061
169 4EES FMN 6.08696
170 6GBV FMN 6.16438
171 3L1N PLM 6.17647
172 4OAS 2SW 6.25
173 4I90 CHT 6.27063
174 1HSL HIS 6.30252
175 1XZ3 ICF 6.32184
176 2GWH PCI 6.37584
177 6BYM HC3 6.40394
178 5M37 9SZ 6.52174
179 4MIX UD1 6.54762
180 5M36 9SZ 6.55022
181 2AF6 BRU 6.58915
182 3SQP 3J8 6.76471
183 4OKD GLC GLC GLC 6.76471
184 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 6.86275
185 5V03 658 6.86275
186 5K7H IVC 6.92641
187 4V1T ADP 7.05882
188 3B99 U51 7.05882
189 2Q1H AS4 7.2
190 5YIZ EF2 7.20721
191 5YJ1 6EL 7.20721
192 5YJ0 EF2 7.20721
193 4WKI 3PW 7.23404
194 3P9T TCL 7.30594
195 4GCZ FMN 7.35294
196 1ZEI CRS 7.54717
197 4DE3 DN8 7.60456
198 5TVI O8N 7.6087
199 5UC1 486 7.65766
200 1NHZ 486 7.85714
201 2YJD YJD 7.91667
202 1J78 VDY 7.94118
203 3CEV ARG 8.02676
204 2CB8 MYA 8.04598
205 4V1F BQ1 8.13953
206 2BHW NEX 8.18966
207 1NU4 MLA 8.24742
208 4RYV ZEA 8.3871
209 1X0P FAD 8.39161
210 5Y02 HBX 8.41121
211 5LWY OLB 8.56164
212 3SP6 IL2 8.77193
213 1MID LAP 8.79121
214 2WH8 II2 8.82353
215 3G4Q MCH 8.90411
216 3RET SAL 8.91089
217 3RET PYR 8.91089
218 3JRS A8S 9.13461
219 2Z6D FMN 9.23077
220 4LWU 20U 9.41177
221 5C1M 4VO 9.45946
222 4RLT FSE 9.52381
223 2RH1 CLR 9.70588
224 2RH1 CAU 9.70588
225 4OGQ 1O2 9.76744
226 4OGQ SQD 9.76744
227 4OGQ 2WD 9.76744
228 4OGQ 7PH 9.76744
229 4OGQ UMQ 9.76744
230 2HFN FMN 9.80392
231 5A4W QCT 9.90566
232 5C9J DAO 9.96441
233 6MVU K4V 10
234 5OM2 DXT 10
235 1BWO LPC 10
236 6AP6 TLF 10.4089
237 4ZGM 32M 10.6557
238 3E70 GDP 10.8824
239 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 11.3139
240 3RY9 1CA 11.6
241 4IBF 1D5 11.6279
242 1ID0 ANP 11.8421
243 1DKF BMS 11.9149
244 1DKF OLA 11.9149
245 6BJO DUY 12
246 4XCP PLM 12.3529
247 4R57 ACO 12.5
248 3P5P A3C 12.6471
249 1SR7 MOF 13.1274
250 5CHR 4NC 13.1387
251 3IX9 MTX 13.1579
252 4OAR 2S0 13.1783
253 3SE5 ANP 13.4146
254 1XX4 BAM 13.7931
255 2V5E SCR 13.8614
256 5TWO 7MV 13.9706
257 2PRG BRL 14.0221
258 3NMV PYV 14.0449
259 4URX FK1 14.5946
260 2Z6C FMN 15.5039
261 4Q86 AMP 15.5882
262 4E2J MOF 16
263 6BVM EBV 16.1677
264 6BVL EBY 16.1677
265 6BVI EC4 16.1677
266 6BVJ EAS 16.1677
267 6BVK EAV 16.1677
268 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 17.3469
269 5N8V KZZ 17.3913
270 4LSJ LSJ 17.8295
271 2GBB CIT 17.9487
272 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 17.9916
273 4I67 G G G RPC 18.3908
274 3LLZ GAL NGA 18.797
275 2HJ3 FAD 20.8
276 5U1M ACE LEU TYR ALA SER SER ASN PRO ALA PTR 20.9524
277 5NNT DPV 21.6216
278 3RMK BML 21.6867
279 5DJT FMN 24.5902
280 4NTO 1PW 24.6377
281 2DYS PGV 25.8503
282 5ZCO PEK 25.8503
283 2DYR PGV 25.8503
284 5Z84 TGL 25.8503
285 2DYS TGL 25.8503
286 2DYR TGL 25.8503
287 1M2Z BOG 28.5714
288 3GN8 DEX 28.5714
289 5SVV FMN 30.6569
290 1NRL SRL 32
291 3BEJ MUF 32
292 1HBK MYR 32.5843
293 2HFP NSI 33.3333
294 1K7L 544 33.3333
295 2J1P GRG 38.2253
296 3KPE TM3 38.4615
297 3T03 3T0 38.8889
298 6A5Y 9CR 43.75
299 1YYE 196 46.1538
300 1U3R 338 46.1538
301 3ET1 ET1 50
302 3ET3 ET1 50
APoc FAQ
Feedback