Receptor
PDB id Resolution Class Description Source Keywords
3ELC 2.5 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSP SYNTHASE COMPLEXED WITH LIGAND ESCHERICHIA COLI K-12 MECDP-SYNTHASE ISOPRENE BIOSYNTHESIS LYASE MAGNESIUM MANMETAL-BINDING
Ref.: A STRUCTURE-BASED APPROACH TO LIGAND DISCOVERY FOR 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHAS TARGET FOR ANTIMICROBIAL THERAPY J.MED.CHEM. V. 52 2531 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
F01 A:901;
B:902;
C:903;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 2.02 mM
261.207 C9 H12 F N3 O5 C1=C(...
GPP C:904;
 Valid;
 none;
 submit data
314.209 C10 H20 O7 P2 CC(=C...
ZN A:801;
B:802;
C:803;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AMT 2.3 Å EC: 4.6.1.12 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH A CDP DERIVED FLUORESCENT INHIBITOR ESCHERICHIA COLI ISOPRENOID LYASE ISOPRENE BIOSYNTHESIS
Ref.: FLUORESCENT INHIBITORS FOR ISPF, AN ENZYME IN THE NON-MEVALONATE PATHWAY FOR ISOPRENOID BIOSYNTHESIS AND A POTENTIAL TARGET FOR ANTIMALARIAL THERAPY. ANGEW.CHEM.INT.ED.ENGL. V. 45 1069 2006
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
2 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
3 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
4 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
5 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
6 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
7 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
8 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
9 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
3 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
6 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
7 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
8 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
11 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
12 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
13 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
14 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
15 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
16 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
17 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
18 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
19 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
20 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
3 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
7 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
8 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
9 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
11 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
12 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
13 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
14 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
15 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
16 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
17 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
18 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
19 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
20 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
21 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
22 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
23 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
24 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
25 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
26 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
27 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: F01; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 F01 1 1
2 B86 0.53125 0.914286
3 5AE 0.52459 0.865672
4 CTN 0.516129 0.924242
5 AR3 0.516129 0.924242
6 5UD 0.492063 0.925373
7 5HM 0.465753 0.815789
8 CTD 0.460317 0.848485
9 TKW 0.458333 0.8
10 ETV 0.455882 0.847222
11 GPK 0.447761 0.882353
12 DKZ 0.408451 0.910448
13 ZEB 0.4 0.850746
Ligand no: 2; Ligand: GPP; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 ZTP 0.911111 0.95
3 GRG 0.911111 0.974359
4 VTP 0.911111 0.95
5 OTP 0.911111 0.95
6 FPP 0.911111 0.974359
7 HZZ 0.704545 0.921053
8 FFF 0.672727 0.904762
9 FJP 0.659574 0.897436
10 0K3 0.659574 0.875
11 DSL 0.659574 0.875
12 FDF 0.654545 0.880952
13 10E 0.617021 0.717391
14 10D 0.617021 0.804878
15 DMA 0.613636 0.868421
16 H6P 0.595745 0.804878
17 10G 0.583333 0.785714
18 A4S 0.545455 0.711538
19 FPF 0.533333 0.904762
20 2CF 0.533333 0.904762
21 FGG 0.52459 0.904762
22 GST 0.518519 0.878049
23 3E9 0.516129 0.926829
24 ELU 0.507937 0.926829
25 ELR 0.507937 0.926829
26 MGM 0.5 0.745098
27 FPS 0.482759 0.857143
28 GGS 0.482759 0.857143
29 FPQ 0.47619 0.804348
30 0FV 0.473684 0.926829
31 LA6 0.473684 0.926829
32 749 0.461538 0.871795
33 1NH 0.444444 0.787234
34 FII 0.444444 0.649123
35 SZH 0.432432 0.637931
36 PS7 0.426667 0.883721
37 9GB 0.42 0.846154
38 C0X 0.41791 0.723404
39 FHP 0.403509 0.738095
40 9AX 0.4 0.826087
Similar Ligands (3D)
Ligand no: 1; Ligand: F01; Similar ligands found: 159
No: Ligand Similarity coefficient
1 THM 0.9801
2 URI 0.9690
3 0DN 0.9640
4 5BT 0.9622
5 DUR 0.9612
6 3BH 0.9601
7 5AD 0.9593
8 MCY 0.9586
9 ADN 0.9577
10 1DA 0.9573
11 TBN 0.9572
12 A 0.9565
13 NOS 0.9562
14 TMC 0.9560
15 I5A 0.9555
16 TIZ 0.9555
17 DCZ 0.9521
18 2TU 0.9512
19 5MD 0.9510
20 A4D 0.9509
21 IMH 0.9508
22 URD 0.9504
23 5CD 0.9502
24 UA2 0.9495
25 ID2 0.9490
26 PRH 0.9484
27 HPR 0.9484
28 PUR 0.9482
29 SCT 0.9479
30 XYA 0.9468
31 6MD 0.9465
32 TYU 0.9458
33 FMC 0.9450
34 TIA 0.9450
35 DBM 0.9442
36 NNR 0.9442
37 UUA 0.9434
38 5NB 0.9429
39 FTU 0.9424
40 GEO 0.9419
41 3D1 0.9393
42 EKH 0.9389
43 THU 0.9388
44 5I5 0.9371
45 4UO 0.9364
46 5ID 0.9356
47 GMP 0.9354
48 3DT 0.9324
49 RFZ 0.9311
50 MTP 0.9307
51 H7S 0.9301
52 CL9 0.9286
53 DDU 0.9283
54 AHU 0.9255
55 DHZ 0.9240
56 W29 0.9235
57 MTA 0.9233
58 7D7 0.9187
59 GNG 0.9174
60 AD3 0.9159
61 BRD 0.9145
62 ZYV 0.9136
63 CC5 0.9135
64 MG7 0.9105
65 AZZ 0.9095
66 HO4 0.9087
67 3L1 0.9083
68 DCF 0.9080
69 BVD 0.9072
70 26A 0.9058
71 N8M 0.9025
72 9UL 0.9022
73 CDY 0.9018
74 TO1 0.9012
75 7CI 0.8992
76 MCF 0.8985
77 TRP 0.8984
78 ACE TRP 0.8983
79 M2T 0.8982
80 PF1 0.8955
81 ZYW 0.8955
82 6J9 0.8944
83 SY4 0.8932
84 ZIQ 0.8917
85 5JT 0.8905
86 F16 0.8899
87 8HG 0.8895
88 EXR 0.8875
89 DTR 0.8871
90 FWD 0.8828
91 BZM 0.8821
92 4OG 0.8817
93 OCZ 0.8810
94 AX8 0.8802
95 CWD 0.8797
96 X11 0.8780
97 WVV 0.8779
98 3Y7 0.8776
99 89J 0.8775
100 PQT 0.8766
101 YOF 0.8766
102 DAH 0.8764
103 LLT 0.8763
104 A4G 0.8759
105 U 0.8755
106 M02 0.8754
107 HBI 0.8750
108 22L 0.8748
109 M5H 0.8742
110 AUV 0.8741
111 5V7 0.8741
112 GA2 0.8740
113 GN6 0.8737
114 0FR 0.8734
115 H4B 0.8729
116 IMQ 0.8726
117 4GU 0.8724
118 6J3 0.8714
119 WOE 0.8708
120 KCH 0.8707
121 SGV 0.8706
122 UVC 0.8705
123 DTE 0.8699
124 IQQ 0.8696
125 CMP 0.8693
126 QQY 0.8688
127 U5P 0.8687
128 HNL 0.8683
129 TI7 0.8682
130 9MR 0.8682
131 ACK 0.8681
132 FTV 0.8679
133 ALN 0.8677
134 SP1 0.8676
135 W8G 0.8665
136 MXD 0.8662
137 NIY 0.8658
138 I2E 0.8648
139 BWD 0.8648
140 27M 0.8646
141 IWD 0.8644
142 EZN 0.8622
143 A1Y 0.8617
144 2GD 0.8614
145 B2T 0.8611
146 6GR 0.8607
147 17C 0.8607
148 JF1 0.8603
149 TMP 0.8599
150 MUK 0.8596
151 C5P 0.8592
152 LTN 0.8583
153 8DA 0.8576
154 JMQ 0.8570
155 SGP 0.8568
156 WS6 0.8561
157 GAL FUC 0.8549
158 WV7 0.8538
159 C2P 0.8535
Ligand no: 2; Ligand: GPP; Similar ligands found: 2
No: Ligand Similarity coefficient
1 RZ5 0.8765
2 86B 0.8716
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AMT; Ligand: 1AA; 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: 2amt.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2AMT; Ligand: 1AA; 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: 2amt.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2AMT; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2amt.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2AMT; Ligand: 1AA; 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: 2amt.bio1) has 60 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2AMT; Ligand: 1AA; 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: 2amt.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2AMT; Ligand: 1AA; 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: 2amt.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2AMT; Ligand: GPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2amt.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2amt.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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