Receptor
PDB id Resolution Class Description Source Keywords
3ern 2.1 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4- CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH ARACMP ESCHERICHIA COLI K-12 MECDP-SYNTHASE ISOPRENE BIOSYNTHESIS LYASE MAGNESIUM MANGANESE METAL-BINDING
Ref.: A STRUCTURE-BASED APPROACH TO LIGAND DISCOVERY FOR 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE: A 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
CAR A:900;
B:900;
C:900;
D:900;
E:900;
 Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
 Kd = 18.91 mM
323.197 C9 H14 N3 O8 P C1=CN...
GPP B:901;
F:902;
 Valid;
Valid;
 none;
none;
 submit data
314.209 C10 H20 O7 P2 CC(=C...
SO4 B:801;
E:801;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
ZN A:800;
B:800;
D:800;
E:800;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
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: CAR; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 C5P 1 1
2 CAR 1 1
3 C 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 HF4 0.753623 0.985507
7 CDP MG 0.735294 0.956522
8 2TM 0.732394 0.944444
9 0RC 0.689189 0.905405
10 7XL 0.689189 0.930556
11 16B 0.676471 0.930556
12 AR3 0.672131 0.842857
13 CTN 0.672131 0.842857
14 C2G 0.662338 0.943662
15 I5A 0.634921 0.828571
16 C5G 0.634146 0.930556
17 CDC 0.62963 0.8375
18 CDM 0.621951 0.881579
19 CXY 0.607143 0.930556
20 TKW 0.591549 0.985507
21 C3P 0.585714 0.956522
22 CDP RB0 0.581395 0.90411
23 5HM 0.575342 0.944444
24 U5P 0.571429 0.941176
25 U 0.571429 0.941176
26 CSQ 0.555556 0.917808
27 CSV 0.555556 0.917808
28 1AA 0.554348 0.893333
29 FZQ 0.548781 0.785714
30 A7R 0.542553 0.917808
31 C2P 0.541667 0.942857
32 PMT 0.540816 0.860759
33 DC 0.540541 0.902778
34 DCM 0.540541 0.902778
35 HQ5 0.523256 0.767442
36 DKZ 0.521127 0.733333
37 YSC 0.5 0.776471
38 G G 6MZ C 0.5 0.825
39 91P 0.495146 0.839506
40 FN5 0.495146 0.858974
41 DOC 0.493333 0.902778
42 5BU 0.486842 0.876712
43 ICR 0.486842 0.861111
44 2AA 0.485714 0.683673
45 MCN 0.485714 0.807229
46 GPC 0.481481 0.829268
47 NCC 0.481132 0.905405
48 G C 0.481132 0.848101
49 5FU 0.48 0.876712
50 CSF 0.476636 0.858974
51 PCD 0.464286 0.770115
52 C5P SIA 0.458716 0.88
53 YYY 0.451219 0.890411
54 UDP 0.45 0.927536
55 CNU 0.45 0.915493
56 44P 0.448718 0.888889
57 DCP 0.447059 0.890411
58 GTF 0.436782 0.890411
59 V12 0.43617 0.7375
60 NUP 0.435897 0.929577
61 GCQ 0.435294 0.890411
62 UTP 0.433735 0.927536
63 2KH 0.428571 0.901408
64 U5F 0.428571 0.927536
65 UP6 0.428571 0.887324
66 NVG 0.427083 0.719512
67 0KX 0.425287 0.866667
68 S5P 0.423077 0.853333
69 GEO 0.418919 0.77027
70 H2U 0.415584 0.861111
71 UDP UDP 0.414634 0.898551
72 FNU 0.4125 0.88
73 JW5 0.4125 0.901408
74 8GM 0.411765 0.906667
75 LDC 0.410959 0.77027
76 DCZ 0.410959 0.77027
77 UPU 0.409091 0.9
78 6MZ C U 0.408 0.825
79 BMP 0.405063 0.901408
80 BMQ 0.402597 0.885714
81 8OP 0.402299 0.853333
82 UNP 0.402299 0.901408
83 DCT 0.402299 0.890411
84 U6M 0.4 0.914286
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: CAR; Similar ligands found: 64
No: Ligand Similarity coefficient
1 UMP 0.9786
2 DU 0.9723
3 TMP 0.9605
4 UFP 0.9564
5 UMC 0.9485
6 9L3 0.9384
7 DUS 0.9346
8 CH 0.9334
9 PSU 0.9319
10 DDN 0.9308
11 AMP 0.9298
12 5IU 0.9288
13 C2R 0.9184
14 2DT 0.9180
15 D4M 0.9180
16 QBT 0.9179
17 NIA 0.9168
18 AIR 0.9159
19 U4S 0.9159
20 AMZ 0.9129
21 NYM 0.9120
22 PFU 0.9105
23 5CM 0.9102
24 BRU 0.9098
25 FDM 0.9070
26 D5M 0.9057
27 DA 0.9057
28 IMP 0.9050
29 FMP 0.9019
30 AS 0.9016
31 IRP 0.8978
32 FAI 0.8945
33 IRN 0.8943
34 NCN 0.8942
35 NMN 0.8941
36 6CN 0.8940
37 GAR 0.8918
38 DGP 0.8876
39 T3S 0.8865
40 5GP 0.8849
41 6MA 0.8835
42 8BR 0.8834
43 OMP 0.8824
44 U3S 0.8812
45 U1S 0.8812
46 NEC 0.8806
47 6AU 0.8800
48 M2T 0.8794
49 5HU 0.8794
50 PZB 0.8774
51 XMP 0.8755
52 2OM 0.8751
53 G 0.8721
54 71V 0.8718
55 DG 0.8676
56 N5O 0.8670
57 MTA 0.8667
58 FDP 0.8652
59 ATM 0.8652
60 2GE 0.8632
61 DUD 0.8609
62 7D5 0.8608
63 TYD 0.8608
64 O8M 0.8552
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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