Receptor
PDB id Resolution Class Description Source Keywords
5HC8 1.87 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LAVANDULYL DIPHOSPHATE SYNTHASE FROM LA INTERMEDIA IN COMPLEX WITH DIMETHYLALLYL DIPHOSPHATE LAVANDULA LANATA SUBSTRATE BINDING PRENYLTRANSFERASE SUBSTRATE TRANSFERASE
Ref.: STRUCTURE AND FUNCTION OF A "HEAD-TO-MIDDLE" PRENYLTRANSFERASE: LAVANDULYL DIPHOSPHATE SYNTHASE ANGEW.CHEM.INT.ED.ENGL. V. 55 4721 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
PIS A:402;
 Valid;
 none;
 submit data
193.033 H3 O6 P2 S OP(=O...
SO4 A:404;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
61G A:403;
 Valid;
 none;
 submit data
68.117 C5 H8 CC(=C...
ISY A:405;
 Valid;
 none;
 submit data
262.158 C5 H12 O6 P2 S CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5HC8 1.87 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LAVANDULYL DIPHOSPHATE SYNTHASE FROM LA INTERMEDIA IN COMPLEX WITH DIMETHYLALLYL DIPHOSPHATE LAVANDULA LANATA SUBSTRATE BINDING PRENYLTRANSFERASE SUBSTRATE TRANSFERASE
Ref.: STRUCTURE AND FUNCTION OF A "HEAD-TO-MIDDLE" PRENYLTRANSFERASE: LAVANDULYL DIPHOSPHATE SYNTHASE ANGEW.CHEM.INT.ED.ENGL. V. 55 4721 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
2 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
2 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
15 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
16 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
17 6IME - GST C10 H20 O6 P2 S CC(=CCCC(=....
18 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
19 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
20 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
21 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
22 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
23 4U82 ic50 = 1.9 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
24 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
25 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
26 6SZG - M2K C8 H10 N2 O2 C1CCc2c(c(....
27 6ACS - CIT C6 H8 O7 C(C(=O)O)C....
28 6SZH - M2H C7 H8 N2 Cc1cc([nH]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PIS; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PIS 1 1
2 PPV 0.642857 0.84
3 3PO 0.5 0.84
4 6YW 0.45 0.84
5 9PI 0.45 0.84
6 PPK 0.409091 0.617647
Ligand no: 2; Ligand: 61G; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 61G 1 1
Ligand no: 3; Ligand: ISY; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 ISY 1 1
2 IPE 0.487805 0.85
3 DST 0.452381 0.820513
4 IP8 0.435897 0.775
Similar Ligands (3D)
Ligand no: 1; Ligand: PIS; Similar ligands found: 165
No: Ligand Similarity coefficient
1 POP 0.9955
2 2PN 0.9951
3 MDN 0.9892
4 MPD 0.9502
5 1GP 0.9486
6 LLQ 0.9473
7 S0H 0.9471
8 FCN 0.9455
9 TB6 0.9441
10 PCT 0.9423
11 7VD 0.9420
12 CP 0.9400
13 SAT 0.9378
14 PAE 0.9374
15 G3P 0.9348
16 G3H 0.9348
17 PGA 0.9285
18 GZ3 0.9282
19 GG6 0.9282
20 OPE 0.9264
21 1DQ 0.9241
22 G2H 0.9235
23 PAH 0.9235
24 TFS 0.9217
25 HX2 0.9193
26 PPR 0.9187
27 H95 0.9176
28 3SL 0.9172
29 X1S 0.9164
30 PEP 0.9157
31 MLI 0.9147
32 MLA 0.9131
33 SIN 0.9129
34 FUM 0.9117
35 13P 0.9102
36 PEQ 0.9101
37 0V5 0.9101
38 3PP 0.9075
39 ITN 0.9062
40 IVA 0.9033
41 3Q7 0.9030
42 A20 0.9030
43 4MV 0.9026
44 CMS 0.9017
45 MLT 0.9001
46 MLM 0.8992
47 LEU 0.8984
48 LMR 0.8980
49 ASP 0.8970
50 2RH 0.8970
51 2PG 0.8960
52 SPV 0.8959
53 SHF 0.8957
54 AAE 0.8951
55 TEO 0.8950
56 FLA 0.8948
57 MAE 0.8943
58 ACH 0.8941
59 ODV 0.8935
60 DCL 0.8930
61 CHT 0.8928
62 ASN 0.8921
63 IPU 0.8919
64 PMB 0.8918
65 COI 0.8909
66 TZC 0.8902
67 2PC 0.8900
68 1DV 0.8899
69 FB2 0.8899
70 2HE 0.8898
71 PSE 0.8888
72 C5J 0.8888
73 HYP 0.8885
74 JBN 0.8881
75 ICF 0.8879
76 DMV 0.8878
77 TFB 0.8878
78 XPO 0.8877
79 RB5 0.8876
80 1SA 0.8874
81 KVV 0.8871
82 GP9 0.8865
83 GLU 0.8864
84 P22 0.8851
85 HIO 0.8850
86 COM 0.8849
87 DMG 0.8848
88 SKG 0.8846
89 DAS 0.8846
90 PRO 0.8840
91 TAU 0.8839
92 3HL 0.8839
93 SRT 0.8834
94 1SH 0.8834
95 SMV 0.8831
96 3PG 0.8830
97 PAF 0.8828
98 BTL 0.8827
99 UY7 0.8824
100 3HR 0.8823
101 P7I 0.8823
102 VX 0.8819
103 FJO 0.8818
104 98J 0.8815
105 SEP 0.8805
106 IHG 0.8804
107 PYC 0.8803
108 BAM 0.8802
109 HDA 0.8799
110 8X3 0.8793
111 HZP 0.8793
112 T2C 0.8792
113 IZC 0.8787
114 FMS 0.8785
115 EFS 0.8780
116 HSM 0.8777
117 BAE 0.8762
118 ETM 0.8761
119 OAA 0.8761
120 PGH 0.8759
121 P2D 0.8755
122 GLN 0.8755
123 MEQ 0.8753
124 TP5 0.8745
125 POA 0.8743
126 PRS 0.8740
127 DGL 0.8728
128 VAL 0.8727
129 GLY ALA 0.8725
130 FOA 0.8718
131 BNS 0.8716
132 KPL 0.8716
133 IQ0 0.8713
134 ALO 0.8707
135 ILE 0.8705
136 TLA 0.8701
137 BEN 0.8700
138 ABU 0.8699
139 C21 0.8694
140 273 0.8692
141 CIZ 0.8685
142 UYA 0.8680
143 A09 0.8677
144 7WG 0.8676
145 6PC 0.8674
146 TAR 0.8674
147 NCA 0.8667
148 1DU 0.8663
149 XLS 0.8653
150 KIV 0.8645
151 IOM 0.8639
152 CRN 0.8639
153 YCP 0.8632
154 SSN 0.8628
155 9X6 0.8624
156 PCA 0.8621
157 THR 0.8611
158 O7U 0.8594
159 DTL 0.8584
160 MRY 0.8577
161 QSC 0.8567
162 M58 0.8560
163 2AS 0.8554
164 HIS 0.8542
165 SS2 0.8541
Ligand no: 2; Ligand: 61G; Similar ligands found: 210
No: Ligand Similarity coefficient
1 F3V 1.0000
2 2A3 1.0000
3 ALA 1.0000
4 GLV 1.0000
5 FAH 1.0000
6 GLY 1.0000
7 PPI 1.0000
8 HAE 1.0000
9 GOA 1.0000
10 HVB 0.9988
11 F50 0.9986
12 TSZ 0.9978
13 R3W 0.9972
14 MGX 0.9972
15 ATO 0.9961
16 2A1 0.9961
17 AGU 0.9947
18 NHY 0.9940
19 NIE 0.9938
20 NMU 0.9934
21 AKR 0.9933
22 BRP 0.9932
23 TCV 0.9923
24 1BP 0.9890
25 J3K 0.9820
26 CP2 0.9771
27 BXA 0.9720
28 3GR 0.9660
29 GOL 0.9658
30 AF3 0.9597
31 AOA 0.9573
32 9A4 0.9570
33 PYR 0.9565
34 LAC 0.9536
35 OXM 0.9504
36 2OP 0.9497
37 BUA 0.9495
38 HBS 0.9490
39 NIS 0.9488
40 DAL 0.9482
41 CYS 0.9480
42 MEU 0.9474
43 5Y9 0.9465
44 OXL 0.9459
45 ACM 0.9455
46 SEY 0.9453
47 HGY 0.9442
48 MMU 0.9436
49 ABA 0.9435
50 BAL 0.9431
51 OXD 0.9429
52 BUO 0.9428
53 3MT 0.9414
54 ACT 0.9409
55 2HA 0.9393
56 GXV 0.9383
57 PYM 0.9382
58 PXO 0.9376
59 BAQ 0.9375
60 CNH 0.9369
61 ALF 0.9369
62 TF4 0.9363
63 AMT 0.9353
64 KCS 0.9345
65 MCH 0.9345
66 1CB 0.9344
67 ALQ 0.9342
68 EDO 0.9310
69 3TR 0.9307
70 ATQ 0.9302
71 3CL 0.9301
72 GBL 0.9295
73 D2P 0.9289
74 5MP 0.9280
75 MR3 0.9277
76 OSM 0.9274
77 NAK 0.9273
78 BEF 0.9270
79 HOW 0.9265
80 2AI 0.9262
81 MZY 0.9261
82 1MZ 0.9255
83 4MZ 0.9254
84 2MZ 0.9254
85 TB0 0.9245
86 NOE 0.9236
87 BRJ 0.9229
88 3OH 0.9227
89 ITU 0.9221
90 78T 0.9220
91 ETF 0.9219
92 HSW 0.9219
93 HBR 0.9218
94 BU4 0.9217
95 2PO 0.9217
96 5KX 0.9210
97 AXO 0.9203
98 VSO 0.9201
99 VN4 0.9199
100 DXX 0.9196
101 JZ6 0.9192
102 BUB 0.9184
103 IPA 0.9180
104 CRD 0.9179
105 EGD 0.9175
106 SLP 0.9167
107 BUQ 0.9164
108 TAN 0.9164
109 SAR 0.9160
110 MTG 0.9139
111 BMD 0.9137
112 6SP 0.9123
113 XAP 0.9120
114 DGY 0.9113
115 HIU 0.9111
116 3ZS 0.9110
117 BYZ 0.9109
118 ES3 0.9107
119 SER 0.9106
120 24T 0.9099
121 3BB 0.9075
122 HYN 0.9065
123 MSF 0.9064
124 DSN 0.9058
125 IMD 0.9050
126 PZO 0.9042
127 HUH 0.9036
128 PYZ 0.9034
129 2KT 0.9031
130 8FH 0.9027
131 MB3 0.9026
132 XIX 0.9023
133 KG7 0.9019
134 DTI 0.9016
135 MMZ 0.9010
136 TRI 0.9005
137 25T 0.9003
138 DMI 0.8999
139 HSL 0.8987
140 1AC 0.8984
141 DCE 0.8981
142 CEJ 0.8976
143 QPT 0.8971
144 B20 0.8968
145 E60 0.8964
146 2RA 0.8956
147 CXL 0.8950
148 BNZ 0.8947
149 PHZ 0.8947
150 0PY 0.8944
151 9A7 0.8944
152 KSW 0.8938
153 13D 0.8933
154 P1R 0.8928
155 DE2 0.8926
156 A3B 0.8925
157 DBB 0.8925
158 03W 0.8923
159 DCY 0.8916
160 CYH 0.8912
161 HUI 0.8897
162 3PY 0.8895
163 HV2 0.8894
164 7EX 0.8892
165 C2N 0.8882
166 HAI 0.8878
167 MBN 0.8877
168 9PO 0.8874
169 HRZ 0.8873
170 SMB 0.8872
171 IPH 0.8864
172 MMQ 0.8863
173 4AX 0.8862
174 2AP 0.8862
175 NVI 0.8861
176 3AP 0.8857
177 HVK 0.8850
178 73M 0.8849
179 3BR 0.8847
180 39J 0.8844
181 V1L 0.8838
182 WOT 0.8835
183 A2Q 0.8835
184 4AP 0.8831
185 LGA 0.8824
186 CHT 0.8816
187 1DH 0.8815
188 8CL 0.8807
189 GXE 0.8804
190 2IM 0.8801
191 MTD 0.8796
192 MZ0 0.8794
193 FW5 0.8782
194 MLI 0.8763
195 3HL 0.8763
196 THR 0.8761
197 MLA 0.8757
198 BVC 0.8757
199 TTO 0.8744
200 HHN 0.8744
201 DMG 0.8737
202 93B 0.8736
203 L60 0.8723
204 PIH 0.8672
205 1SP 0.8671
206 C5J 0.8668
207 CPT 0.8638
208 TAY 0.8629
209 AAE 0.8593
210 3HR 0.8583
Ligand no: 3; Ligand: ISY; Similar ligands found: 24
No: Ligand Similarity coefficient
1 IPR 0.9280
2 IS3 0.9222
3 DMA 0.9217
4 DED 0.9214
5 EIP 0.9073
6 0CM 0.9014
7 0O3 0.8994
8 0CH 0.8959
9 0CN 0.8892
10 10G 0.8882
11 P25 0.8836
12 2JA 0.8823
13 6FR 0.8816
14 BHI 0.8759
15 58X 0.8741
16 AHL 0.8740
17 0JX 0.8740
18 HPO 0.8731
19 PMV 0.8727
20 10E 0.8720
21 3CX 0.8680
22 2E5 0.8675
23 PTB 0.8657
24 ARG 0.8630
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HC8; Ligand: 61G; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5hc8.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5XK9 GST 43.9655
Pocket No.: 2; Query (leader) PDB : 5HC8; Ligand: 61G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5hc8.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5HC8; Ligand: PIS; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 5hc8.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5XK9 GST 43.9655
2 5XK9 DMA 43.9655
3 5XK9 DMA 43.9655
Pocket No.: 4; Query (leader) PDB : 5HC8; Ligand: PIS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5hc8.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5HC8; Ligand: ISY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5hc8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5HC8; Ligand: ISY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5hc8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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