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 7 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 (41)
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 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
4 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
5 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
6 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
7 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
8 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
9 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
10 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
11 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
12 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
13 3N45 - PO4 O4 P [O-]P(=O)(....
14 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
15 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
16 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
18 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
19 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
20 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
21 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
22 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
24 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
25 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
27 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
28 3N46 - PO4 O4 P [O-]P(=O)(....
29 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
30 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
31 4H5C - PO4 O4 P [O-]P(=O)(....
32 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
33 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
34 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
35 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
36 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
37 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
38 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
39 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
40 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
41 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (65)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 = 6 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 Kd = 9.2 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 Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
13 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
14 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
15 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
16 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
17 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
18 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
19 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
20 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
22 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
23 3N46 - PO4 O4 P [O-]P(=O)(....
24 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
25 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
26 4H5C - PO4 O4 P [O-]P(=O)(....
27 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
28 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
29 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
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 6B07 - C6M C10 H18 N O6 P2 CCC[N]1=C(....
35 6B04 - C6J C8 H14 N O6 P2 C[N]1=C(C=....
36 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
37 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
38 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
39 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
40 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
41 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
42 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
43 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
44 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
45 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
46 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
47 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
48 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
49 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
50 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
51 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
52 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
53 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
54 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
55 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
56 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
57 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
58 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
59 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
60 4DWB ic50 = 1840 nM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
61 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
62 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
63 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
64 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
65 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands (2D)
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 FPP 0.5625 0.846154
9 GRG 0.5625 0.846154
10 ZTP 0.5625 0.825
11 VTP 0.5625 0.825
12 OTP 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 LA6 0.431373 0.804878
20 0FV 0.431373 0.804878
21 IPE 0.428571 0.794872
Similar Ligands (3D)
Ligand no: 1; Ligand: DMA; Similar ligands found: 138
No: Ligand Similarity coefficient
1 IPR 0.9903
2 DED 0.9793
3 DST 0.9657
4 IS3 0.9594
5 0CH 0.9512
6 43W 0.9397
7 0O3 0.9348
8 0K2 0.9338
9 2E5 0.9309
10 2JA 0.9289
11 0CM 0.9286
12 EIP 0.9251
13 2E6 0.9248
14 P3S 0.9241
15 G88 0.9229
16 0CG 0.9223
17 ISY 0.9217
18 2E4 0.9194
19 P25 0.9177
20 PMV 0.9174
21 0JX 0.9158
22 58X 0.9141
23 DLT 0.9129
24 ZZU 0.9127
25 6FR 0.9092
26 RGP 0.9092
27 HPO 0.9088
28 BGT 0.9063
29 BHI 0.9061
30 VFG 0.9001
31 AZM 0.8999
32 27L 0.8983
33 DG2 0.8963
34 NLG 0.8956
35 2E7 0.8949
36 M8O 0.8948
37 5RP 0.8936
38 PUW 0.8925
39 NLQ 0.8925
40 MGB 0.8924
41 2OR 0.8910
42 GGG 0.8906
43 G01 0.8905
44 6C4 0.8895
45 3CX 0.8888
46 5LD 0.8883
47 EGV 0.8875
48 ARG 0.8861
49 DAR 0.8861
50 AX3 0.8860
51 ASF 0.8857
52 M3L 0.8848
53 HSA 0.8836
54 VFM 0.8828
55 NFZ 0.8825
56 6FG 0.8822
57 6C5 0.8820
58 6C8 0.8817
59 TX4 0.8811
60 DI9 0.8807
61 G6Q 0.8803
62 S6P 0.8803
63 5DS 0.8800
64 STX 0.8798
65 64Z 0.8792
66 AHL 0.8792
67 5TO 0.8791
68 PA5 0.8787
69 CH5 0.8784
70 VFJ 0.8772
71 U7E 0.8761
72 PAN 0.8761
73 GRQ 0.8758
74 C26 0.8756
75 HS7 0.8753
76 LEL 0.8742
77 GVA 0.8738
78 5DL 0.8738
79 ALA GLU 0.8732
80 NBB 0.8731
81 P93 0.8723
82 6C9 0.8723
83 0F3 0.8719
84 HJ7 0.8712
85 EXY 0.8710
86 23N 0.8706
87 DNN 0.8704
88 49P 0.8701
89 37E 0.8701
90 RES 0.8700
91 DX5 0.8698
92 ING 0.8696
93 HCA 0.8696
94 0M9 0.8686
95 VM1 0.8685
96 IVL 0.8685
97 3EB 0.8678
98 AGP 0.8672
99 SSM 0.8671
100 DHC 0.8671
101 5SP 0.8669
102 UN1 0.8669
103 PML 0.8665
104 N8C 0.8658
105 9J6 0.8658
106 MZM 0.8652
107 SB7 0.8650
108 KNA 0.8646
109 HRG 0.8645
110 AES 0.8642
111 5F5 0.8636
112 9BF 0.8633
113 DI6 0.8630
114 OKP 0.8625
115 KAP 0.8624
116 NPI 0.8621
117 JF5 0.8618
118 IOP 0.8615
119 PAU 0.8613
120 R52 0.8606
121 TBJ 0.8605
122 A5P 0.8604
123 LX1 0.8601
124 F6R 0.8599
125 0LO 0.8594
126 14W 0.8592
127 MLY 0.8585
128 RIS 0.8585
129 PTB 0.8582
130 VGS 0.8581
131 ZOL 0.8580
132 TB8 0.8578
133 M28 0.8564
134 I2E 0.8554
135 R5P 0.8545
136 7UC 0.8535
137 4NP 0.8522
138 XEN 0.8521
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: 2
This union binding pocket(no: 1) in the query (biounit: 1uby.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4UMJ BFQ 34.1216
2 4UMJ BFQ 34.1216
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: 2
This union binding pocket(no: 3) in the query (biounit: 1uby.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4UMJ BFQ 34.1216
2 4UMJ BFQ 34.1216
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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