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- CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH LIGAND 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
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 ~ 40 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
2 2GZL ic50 = 3 mM 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 (22)
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 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
3 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 3ERN Kd ~ 40 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 2GZL ic50 = 3 mM 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 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
14 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
15 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
16 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
17 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
18 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
19 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
20 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
21 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
22 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
50% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 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 ~ 40 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL ic50 = 3 mM 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 4C81 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
15 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
16 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
17 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
18 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
19 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
20 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
21 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
22 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
23 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
24 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
25 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
26 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
27 1IV2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
28 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
29 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
30 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
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: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 OTP 0.911111 0.95
3 ZTP 0.911111 0.95
4 VTP 0.911111 0.95
5 GRG 0.911111 0.974359
6 FPP 0.911111 0.974359
7 FFF 0.672727 0.904762
8 DSL 0.659574 0.875
9 0K3 0.659574 0.875
10 FJP 0.659574 0.897436
11 FDF 0.654545 0.880952
12 10D 0.617021 0.804878
13 10E 0.617021 0.717391
14 DMA 0.613636 0.868421
15 H6P 0.595745 0.804878
16 10G 0.583333 0.785714
17 A4S 0.545455 0.711538
18 2CF 0.533333 0.904762
19 FPF 0.533333 0.904762
20 FGG 0.52459 0.904762
21 GST 0.518519 0.878049
22 3E9 0.516129 0.926829
23 MGM 0.5 0.745098
24 FPS 0.482759 0.857143
25 GGS 0.482759 0.857143
26 FPQ 0.47619 0.804348
27 LA6 0.473684 0.926829
28 0FV 0.473684 0.926829
29 749 0.461538 0.871795
30 1NH 0.444444 0.787234
31 FII 0.444444 0.649123
32 SZH 0.432432 0.637931
33 PS7 0.426667 0.883721
34 FHP 0.403509 0.738095
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2AMT; Ligand: GPP; Similar sites found: 55
This union binding pocket(no: 3) in the query (biounit: 2amt.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XMY ROL 0.008629 0.42936 None
2 5A67 3PO 0.01185 0.42688 None
3 3P7I P7I 0.0119 0.42678 None
4 3BY9 SIN 0.01682 0.42093 None
5 4QM9 CYS 0.01685 0.41997 None
6 1XM4 PIL 0.01755 0.40571 None
7 3BRN SRO 0.0325 0.40417 None
8 3T2W BTN 0.02579 0.40114 None
9 4MWV BCZ 0.01394 0.40337 1.88679
10 3RDO BTN 0.01867 0.40083 1.96078
11 4WXJ GLU 0.03439 0.40247 2.51572
12 3G58 988 0.02464 0.40213 2.51572
13 4CIB 7UZ 0.008415 0.43621 3.14465
14 2B3B GLC 0.01714 0.4141 3.14465
15 2B3B BGC 0.01787 0.41318 3.14465
16 1A8S PPI 0.03413 0.4094 3.14465
17 5D4Y BXP 0.03706 0.40074 3.14465
18 5HZ9 5M8 0.01366 0.40731 3.7037
19 3H7J PPY 0.0146 0.40592 3.77358
20 4JGP PYR 0.03106 0.40509 3.77358
21 3QH2 3NM 0.01702 0.41861 4.40252
22 2IBN I1N 0.02739 0.41144 4.40252
23 4IAW LIZ 0.0162 0.41125 4.40252
24 1E5Q SHR 0.02096 0.40193 4.40252
25 5LUN ARG 0.03217 0.40003 4.40252
26 4YRD 3IT 0.02698 0.40413 4.45682
27 4QN7 G39 0.00851 0.41709 5.03145
28 5A7V MAN 0.02449 0.41027 5.03145
29 5W0N UPU 0.0259 0.40899 5.03145
30 1F8I GLV 0.02101 0.40855 5.03145
31 2ACO VCA 0.03152 0.40448 5.03145
32 1AJ0 SAN 0.009114 0.40194 5.03145
33 4EKV BTN 0.02146 0.40143 5.03145
34 4B7J G39 0.006125 0.42798 5.66038
35 2OVW CBI 0.01908 0.41171 5.66038
36 1C96 FLC 0.01471 0.40945 5.66038
37 3B00 16A 0.02702 0.40012 5.66038
38 3TI8 LNV 0.01395 0.40004 5.66038
39 1VKF CIT 0.01818 0.42051 6.28931
40 1BZL FAD 0.03543 0.40695 6.28931
41 2Q89 6CS 0.02613 0.40468 6.28931
42 3GM5 CIT 0.03594 0.40239 6.28931
43 4BT5 23B 0.02131 0.40925 6.91824
44 4CPZ ZMR 0.01206 0.40293 6.91824
45 2WHX ADP 0.03848 0.40058 6.91824
46 4M8D 23J 0.0375 0.40047 7.54717
47 4Z7X 3CX 0.02644 0.40307 8.80503
48 4H53 SLB 0.01268 0.40884 9.43396
49 3TIC ZMR 0.01248 0.40562 9.43396
50 4WOE 3S5 0.01561 0.42328 11.9497
51 3MMH SME 0.01602 0.4115 13.7725
52 2XVL PXN 0.02197 0.41286 15.0943
53 1CZA G6P 0.02305 0.40358 16.3522
54 3WJO IPE 0.02085 0.4156 16.9811
55 2VOH CIT 0.005178 0.42084 26.9231
Pocket No.: 4; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 5
This union binding pocket(no: 4) in the query (biounit: 2amt.bio1) has 60 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TLG GAL 0.002231 0.48904 None
2 3KIH GDL 0.01798 0.44748 2.06186
3 3KIF GDL 0.03103 0.43386 5.66038
4 5C2N NAG 0.02967 0.43616 10.4167
5 2Z49 AMG 0.04385 0.41775 15.0943
Pocket No.: 5; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 24
This union binding pocket(no: 5) in the query (biounit: 2amt.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4G0P U5P 0.0251 0.41396 None
2 2GL0 ADN 0.03177 0.4043 None
3 1U4L H1S 0.04776 0.40265 None
4 3DXY SAM 0.02096 0.40193 3.77358
5 4N9Z V3L 0.0356 0.41325 4.40252
6 3HCH RSM 0.04163 0.40102 4.40252
7 1WK8 VMS 0.02019 0.40647 5.03145
8 3IT7 TLA 0.04048 0.40482 5.03145
9 4XJ7 ADN 0.03304 0.40339 5.03145
10 4U60 SIA 0.02926 0.40001 5.03145
11 1FP1 SAH 0.01105 0.40808 5.66038
12 2J0B UDP 0.03043 0.40206 5.66038
13 2X2T GAL NGA 0.03123 0.40415 5.88235
14 3LST SAH 0.007503 0.41969 6.28931
15 2WCI GSH 0.03955 0.40052 6.66667
16 4ISS TAR 0.009423 0.43441 6.91824
17 2CJZ PTR 0.01956 0.41937 6.91824
18 2W8Q SIN 0.02665 0.40986 8.1761
19 3NFD COA 0.0293 0.40212 8.80503
20 2AJH MET 0.02152 0.41392 10.6918
21 5W3X IHP 0.03519 0.40415 10.6918
22 3IWD M2T 0.03669 0.40184 11.2903
23 4CUB GAL NAG 0.02845 0.40243 11.9497
24 1Z03 OCH 0.02185 0.4129 16.3522
Pocket No.: 6; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2AMT; Ligand: GPP; Similar sites found: 2
This union binding pocket(no: 7) in the query (biounit: 2amt.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1A8U BEZ 0.03211 0.40057 5.03145
2 2Q1S NAI 0.02655 0.4023 5.66038
Pocket No.: 8; Query (leader) PDB : 2AMT; Ligand: 1AA; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback