Receptor
PDB id Resolution Class Description Source Keywords
1x07 2.2 Å EC: 2.5.1.31 CRYSTAL STRUCTURE OF UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MG AND IPP ESCHERICHIA COLI ENZYME-SUBSTRATE COMPLEX TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM, ISOPENTENYL PYROPHOSPHATE, AND FARNESYL THIOPYROPHOSPHATE: ROLES OF THE METAL ION AND CONSERVED RESIDUES IN CATALYSIS. J.BIOL.CHEM. V. 280 20762 200
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPE A:901;
Valid;
none;
Kd = 520 uM
246.092 C5 H12 O7 P2 CC(=C...
MG A:900;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:902;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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)....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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)....
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: IPE; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 IPE 1 1
2 IP8 0.617647 0.918919
3 0O3 0.589744 0.871795
4 0CJ 0.536585 0.780488
5 P23 0.527778 0.815789
6 ISY 0.487805 0.85
7 DED 0.487179 0.653061
8 IPR 0.475 0.820513
9 P25 0.463415 0.825
10 P22 0.444444 0.710526
11 43W 0.439024 0.789474
12 0CH 0.439024 0.731707
13 EIP 0.431818 0.846154
14 DMA 0.428571 0.794872
15 0JX 0.428571 0.810811
16 0K2 0.418605 0.74359
17 BHI 0.413043 0.767442
18 DP6 0.408163 0.785714
Similar Ligands (3D)
Ligand no: 1; Ligand: IPE; Similar ligands found: 140
No: Ligand Similarity coefficient
1 IS3 0.9735
2 10D 0.9529
3 10E 0.9483
4 H6P 0.9440
5 10G 0.9433
6 DST 0.9412
7 0CN 0.9411
8 2JA 0.9339
9 0CM 0.9331
10 43Q 0.9304
11 RGP 0.9261
12 P3S 0.9259
13 2E5 0.9200
14 2E4 0.9161
15 AZM 0.9151
16 2E6 0.9145
17 PMV 0.9124
18 DLT 0.9121
19 HPO 0.9081
20 0CG 0.9079
21 BGT 0.9058
22 6FR 0.9052
23 I58 0.9029
24 AGP 0.9018
25 G6Q 0.9009
26 MGB 0.9008
27 G88 0.9005
28 3PO 0.8983
29 DG2 0.8982
30 ATX 0.8980
31 PA5 0.8962
32 M3L 0.8957
33 58X 0.8948
34 5DS 0.8936
35 ZZU 0.8923
36 DI9 0.8915
37 STX 0.8907
38 CXA 0.8892
39 HSA 0.8888
40 DX5 0.8882
41 5SP 0.8881
42 TX4 0.8878
43 5TO 0.8855
44 NLQ 0.8854
45 88L 0.8850
46 PAN 0.8834
47 NFZ 0.8833
48 CIR 0.8833
49 PPK 0.8830
50 5RP 0.8824
51 ARG 0.8824
52 4TP 0.8823
53 ALA GLU 0.8820
54 0F3 0.8819
55 3CX 0.8813
56 GGB 0.8813
57 RES 0.8811
58 ILO 0.8811
59 GGG 0.8808
60 4NP 0.8793
61 2OR 0.8792
62 EGV 0.8790
63 PNP 0.8789
64 PAU 0.8787
65 DAR 0.8787
66 3UF 0.8784
67 NBB 0.8784
68 AHL 0.8776
69 4MB 0.8774
70 R52 0.8774
71 R5P 0.8774
72 CU0 0.8771
73 NLG 0.8757
74 M3C 0.8756
75 3W3 0.8755
76 A5P 0.8753
77 PTB 0.8753
78 GVA 0.8752
79 2J3 0.8749
80 HCT 0.8743
81 5LD 0.8743
82 GRQ 0.8736
83 64Z 0.8733
84 4NS 0.8732
85 HRG 0.8732
86 D5X 0.8731
87 VFG 0.8731
88 3EB 0.8730
89 DXP 0.8730
90 HAR 0.8728
91 HCA 0.8727
92 HLP 0.8723
93 6C5 0.8713
94 MZM 0.8712
95 ASF 0.8709
96 S6P 0.8702
97 DEZ 0.8697
98 6FG 0.8697
99 5OY 0.8693
100 CPM 0.8692
101 PML 0.8691
102 WT2 0.8690
103 1OS 0.8687
104 M28 0.8684
105 B15 0.8675
106 XOG 0.8672
107 KAP 0.8669
108 FSA 0.8669
109 6C8 0.8668
110 2O8 0.8666
111 U4G 0.8663
112 1PS 0.8661
113 5PV 0.8659
114 HJ7 0.8649
115 1FD 0.8647
116 GG8 0.8647
117 LGT 0.8646
118 GAE 0.8643
119 AES 0.8640
120 E79 0.8640
121 IOP 0.8638
122 API 0.8637
123 VUR 0.8637
124 6PG 0.8634
125 3XR 0.8622
126 DER 0.8612
127 U7E 0.8609
128 FM4 0.8605
129 4JE 0.8599
130 23N 0.8596
131 BSC 0.8587
132 GLY GLY GLY 0.8579
133 ING 0.8576
134 2JJ 0.8569
135 EUE 0.8565
136 0QA 0.8564
137 K4V 0.8541
138 LRW 0.8540
139 CS2 0.8539
140 KDG 0.8525
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WYJ; Ligand: H78; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3wyj.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
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