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Receptor
PDB id Resolution Class Description Source Keywords
1UBY 2.4 Å EC: 2.5.1.1 STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE GALLUS GALLUS TRANSFERASE ISOPRENE BIOSYNTHESIS CHOLESTEROL BIOSYNTHESIS
Ref.: REGULATION OF PRODUCT CHAIN LENGTH BY ISOPRENYL DIP SYNTHASES. PROC.NATL.ACAD.SCI.USA V. 93 15018 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMA A:401;
Valid;
none;
submit data
246.092 C5 H12 O7 P2 CC(=C...
MG A:402;
A:403;
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
1UBY 2.4 Å EC: 2.5.1.1 STRUCTURE OF FARNESYL PYROPHOSPHATE SYNTHETASE GALLUS GALLUS TRANSFERASE ISOPRENE BIOSYNTHESIS CHOLESTEROL BIOSYNTHESIS
Ref.: REGULATION OF PRODUCT CHAIN LENGTH BY ISOPRENYL DIP SYNTHASES. PROC.NATL.ACAD.SCI.USA V. 93 15018 1996
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
2 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
3 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
4 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
5 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
6 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
7 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
8 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
9 5JV2 ic50 = 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
10 3N5J ic50 = 8 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
11 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
12 3N45 - PO4 O4 P [O-]P(=O)(....
13 4LPH ic50 = 4.5 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
14 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
15 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
16 4LPG ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
17 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
18 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
19 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
20 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
22 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
24 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
25 3N46 - PO4 O4 P [O-]P(=O)(....
26 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
27 4H5C - PO4 O4 P [O-]P(=O)(....
28 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
29 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
30 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
31 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
32 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
33 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
34 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
35 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
36 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (60)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
4 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
5 5JV2 ic50 = 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
6 3N5J ic50 = 8 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
7 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
8 3N45 - PO4 O4 P [O-]P(=O)(....
9 4LPH ic50 = 4.5 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
10 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
11 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
12 4LPG ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
13 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
14 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
15 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
16 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
18 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
19 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
20 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
21 3N46 - PO4 O4 P [O-]P(=O)(....
22 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
23 4H5C - PO4 O4 P [O-]P(=O)(....
24 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
25 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
27 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
28 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
29 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
30 6B07 - C6M C10 H18 N O6 P2 CCC[N]1=C(....
31 6B04 - C6J C8 H14 N O6 P2 C[N]1=C(C=....
32 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
33 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
34 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
35 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
36 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
37 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
38 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
39 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
40 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
41 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
42 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
43 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
44 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
45 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
46 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
47 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
48 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
49 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
50 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
51 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
52 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
53 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
54 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
55 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
56 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
57 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
58 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
59 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
60 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DMA; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 DMA 1 1
2 H6P 0.684211 0.815789
3 10E 0.666667 0.72093
4 10D 0.625 0.815789
5 10G 0.625 0.794872
6 GPP 0.613636 0.868421
7 4LR 0.588235 0.909091
8 OTP 0.5625 0.825
9 VTP 0.5625 0.825
10 FPP 0.5625 0.846154
11 GRG 0.5625 0.846154
12 ZTP 0.5625 0.825
13 FFF 0.5 0.785714
14 0CN 0.463415 0.771429
15 FDF 0.454545 0.761905
16 P23 0.447368 0.710526
17 P22 0.444444 0.794118
18 0CJ 0.431818 0.682927
19 0FV 0.431373 0.804878
20 LA6 0.431373 0.804878
21 IPE 0.428571 0.794872
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UBY; Ligand: DMA; Similar sites found with APoc: 175
This union binding pocket(no: 1) in the query (biounit: 1uby.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5MT9 SRO None
2 5MT9 ARG None
3 1MT1 AG2 None
4 3KPE TM3 None
5 1U25 IHS 1.18694
6 5V3Y 5V8 1.3986
7 1R6N 434 1.4218
8 6ARJ BW4 1.7192
9 6ARJ SAH 1.7192
10 4OHU NAD 1.7301
11 4OHU 2TK 1.7301
12 6GL8 F3Q 1.74419
13 2HHP FLC 1.90736
14 1EWF PC1 1.90736
15 5XDT ZI7 1.94805
16 2QE4 JJ3 2.01613
17 5B0I BOG 2.04082
18 3GF2 SAL 2.05479
19 4D42 W0I 2.12766
20 4D42 NAP 2.12766
21 5EK3 5PK 2.17984
22 4LY9 S6P 2.17984
23 4LY9 1YY 2.17984
24 3RWP ABQ 2.2508
25 2I0G I0G 2.33463
26 5JIB OIA 2.37389
27 2O1V ADP 2.45232
28 1XMY ROL 2.45232
29 3G58 988 2.45232
30 3B9Z CO2 2.45232
31 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 2.45232
32 4B5P ACO 2.5
33 3KDU NKS 2.52708
34 2P4Y C03 2.52708
35 3SFI 3SF 2.54237
36 3FUR Z12 2.57353
37 3G9E RO7 2.58303
38 4I90 CHT 2.64026
39 3KP6 SAL 2.64901
40 1E4I NFG 2.7248
41 1YQZ FAD 2.7248
42 3E70 GDP 2.7439
43 5X3R 7Y3 2.92683
44 1T27 PCW 2.95203
45 3X01 AMP 2.99728
46 4URX FK1 2.99728
47 2CIX CEJ 3.01003
48 5M36 9SZ 3.05677
49 1M13 HYF 3.16456
50 4U60 SIA GAL NGA 3.21429
51 2BCG GER 3.26975
52 2A1L PCW 3.33333
53 3GZ9 D32 3.34572
54 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 3.36134
55 1U7T TDT 3.44828
56 3EYK EYK 3.48837
57 4KCF AKM 3.54223
58 5V4R MGT 3.7037
59 6BA2 7KM 3.72881
60 6CB2 OLC 3.75427
61 2ZCQ B65 3.75427
62 5OSW DIU 3.81471
63 4WGF HX2 3.90244
64 1GNI OLA 4.08719
65 6C0B PAM 4.08719
66 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 4.1841
67 4TQ3 GPP 4.29043
68 4P6X HCY 4.31373
69 1JGS SAL 4.34783
70 5B4B LP5 4.43548
71 5XJ7 87O 4.47761
72 6BR8 PGV 4.7619
73 6BR8 6OU 4.7619
74 2VWA PTY 4.9505
75 5AZC PGT 5
76 4MNS 2AX 5.03145
77 3KV8 FAH 5.03597
78 2GBB CIT 5.12821
79 4RYV ZEA 5.16129
80 4F4S EFO 5.26316
81 4YSX E23 5.31915
82 2GWH PCI 5.36913
83 4MRP GSH 5.37459
84 1GEG GLC 5.46875
85 5AAV GW5 5.55556
86 6CHP F0Y 5.59006
87 3ZLR X0B 5.6962
88 5UC9 MYR 5.75221
89 2UW1 GVM 5.91716
90 2HZL PYR 5.99455
91 6AYI C3G 6.03015
92 3L9R L9R 6.12245
93 4MGA 27L 6.27451
94 3SCM LGN 6.29139
95 4TV1 36M 6.3745
96 1QM5 PLP 6.53951
97 1SJD NPG 6.53951
98 5Y02 HBX 6.54206
99 3H0A D30 6.57895
100 4G86 BNT 6.69014
101 5F1R 42O 6.75105
102 5W7B MYR 6.81199
103 2WQ4 SFU 7.05128
104 5C1M OLC 7.2
105 3W54 RNB 7.29483
106 3OKI OKI 7.29614
107 5CQG 55C 7.35695
108 4OIV XX9 7.52212
109 5URY PAM 7.53425
110 5TVI O8N 7.6087
111 3B6C SDN 7.69231
112 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 7.84314
113 3G08 FEE 7.90191
114 3QUZ QUV 7.90191
115 5OCA 9QZ 7.93651
116 4J7Q B7N 8.10811
117 1TV5 N8E 8.12641
118 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 8.16327
119 1NF8 BOG 8.21256
120 2E2R 2OH 8.60656
121 6BR9 PGV 8.6351
122 1J78 OLA 8.71935
123 5NTP 98E 8.82353
124 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 8.84354
125 4XTX 590 8.88889
126 3LN0 52B 8.99183
127 4I67 G G G RPC 9.1954
128 1NU4 MLA 9.27835
129 4V1F BQ1 9.30233
130 5LWY OLB 9.34579
131 5IJJ I6P 9.375
132 3RLF MAL 9.53679
133 2D5Z L35 9.92908
134 2WOR 2AN 10
135 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 10
136 5WL1 D3D 10.101
137 5WL1 CUY 10.101
138 5C9J DAO 10.101
139 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 10.101
140 3HUJ AGH 10.101
141 5LX9 OLB 10.2113
142 1L0I PSR 10.2564
143 6BJO DUY 10.4
144 2VZZ SCA 10.5505
145 3O01 DXC 10.7143
146 2BHW NEX 11.2069
147 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 11.8557
148 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 12.3967
149 5TCI 79V 12.5341
150 1XVB BHL 14.1176
151 1XVB 3BR 14.1176
152 3U3U EAH 14.5923
153 2Y69 CHD 15
154 1T0S BML 15.1163
155 3N7S 3N7 15.625
156 5V03 658 15.6863
157 1B4N GUA 15.8038
158 1XZ3 ICF 17.2414
159 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 18.3673
160 5MWE TCE 18.5714
161 4OGQ 7PH 21.6216
162 5Z84 CHD 21.7391
163 5ZCO CHD 21.7391
164 5W97 CHD 21.7391
165 2DYS PGV 21.7391
166 5Z84 PGV 21.7391
167 2Z7I 742 27.9412
168 2J1P GRG 30.7167
169 4UMJ BFQ 34.1216
170 1RQJ RIS 34.4482
171 3WJO IPE 37.6855
172 2O1O RIS 41.4169
173 1YHM AHD 43.6464
174 4JZB P2H 46.9613
175 4JZX 476 46.9613
Pocket No.: 2; Query (leader) PDB : 1UBY; Ligand: DMA; 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: 1uby.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1UBY; Ligand: DMA; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 1uby.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3WYJ H78 3.55731
3 2V5E SCR 42.5743
Pocket No.: 4; Query (leader) PDB : 1UBY; Ligand: DMA; 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: 1uby.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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