Receptor
PDB id Resolution Class Description Source Keywords
3P10 1.7 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOS SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH CYTIDINE AND F( THIOPHEN-2-YL)PHENYL METHANOL BURKHOLDERIA PSEUDOMALLEI SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE SISPF CYTIDINE FOL694 F69 MEP PATHWAY ISOPRENE BIOSYNTHLYASE METAL-BINDING
Ref.: LEVERAGING STRUCTURE DETERMINATION WITH FRAGMENT SC FOR INFECTIOUS DISEASE DRUG TARGETS: MECP SYNTHASE BURKHOLDERIA PSEUDOMALLEI. J STRUCT FUNCT GENOMICS V. 12 63 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:163;
Invalid;
none;
submit data
35.453 Cl [Cl-]
CTN A:165;
B:165;
C:165;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
243.217 C9 H13 N3 O5 C1=CN...
F69 A:170;
Valid;
none;
submit data
190.261 C11 H10 O S c1ccc...
K C:163;
Invalid;
none;
submit data
39.098 K [K+]
ZN A:164;
B:163;
C:164;
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
3JVH 1.69 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSP SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH FOL FRAGMENT 8 BURKHOLDERIA PSEUDOMALLEI NIAID SSGCID SEATTLE DTRUCTURAL GENOMICS CENTER FOR INFECTDISEASE FRAGMENT CRYSTALLOGRAPHY FRAGMENTS OF LIFE ZINC-FRAGMENT ISOPRENE BIOSYNTHESIS LYASE METAL-BINDING STRUGENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS
Ref.: LEVERAGING STRUCTURE DETERMINATION WITH FRAGMENT SC FOR INFECTIOUS DISEASE DRUG TARGETS: MECP SYNTHASE BURKHOLDERIA PSEUDOMALLEI. J STRUCT FUNCT GENOMICS V. 12 63 2011
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
3 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
4 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
6 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
7 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
8 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
9 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
10 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
11 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
12 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)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: CTN; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 CTN 1 1
2 AR3 1 1
3 I5A 0.754717 0.920635
4 DKZ 0.719298 0.863636
5 CAR 0.672131 0.842857
6 C 0.672131 0.842857
7 C5P 0.672131 0.842857
8 C3P 0.655738 0.828571
9 CDP 0.636364 0.857143
10 CTP 0.608696 0.857143
11 C2P 0.603175 0.842857
12 CDP MG 0.57971 0.819444
13 7XL 0.575342 0.859155
14 C2G 0.552632 0.871429
15 CTD 0.551724 0.887097
16 C5G 0.55 0.859155
17 5AE 0.542373 0.935484
18 GEO 0.532258 0.878788
19 C C 0.525641 0.842857
20 DCZ 0.52459 0.907692
21 LDC 0.52459 0.907692
22 CDM 0.518519 0.813333
23 F01 0.516129 0.924242
24 CDC 0.506173 0.728395
25 U 0.5 0.919355
26 URI 0.5 0.919355
27 CSQ 0.494253 0.821918
28 CSV 0.494253 0.821918
29 CXY 0.488095 0.833333
30 NVG 0.476744 0.810811
31 URD 0.47541 0.809524
32 V12 0.470588 0.833333
33 2TU 0.460317 0.848485
34 CJB 0.453125 0.873016
35 LTT 0.453125 0.876923
36 CC7 0.452055 0.802817
37 3TC 0.446154 0.835821
38 1AA 0.445652 0.8
39 16B 0.444444 0.783784
40 ZEB 0.435484 0.919355
41 G C 0.427184 0.759494
42 DC 0.424658 0.756757
43 DCM 0.424658 0.756757
44 DHZ 0.421875 0.919355
45 BRD 0.415385 0.870968
46 GPC 0.415094 0.722892
47 PMT 0.41 0.75
48 MCN 0.403846 0.722892
Ligand no: 2; Ligand: F69; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 F69 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3JVH; Ligand: HHV; Similar sites found: 27
This union binding pocket(no: 1) in the query (biounit: 3jvh.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KIH GDL 0.03532 0.40908 None
2 2QN6 GDP 0.02165 0.41637 3.27869
3 4D79 ATP 0.01268 0.40647 3.27869
4 5OFW 9TW 0.03702 0.40644 3.27869
5 3DXY SAM 0.02011 0.41033 3.82514
6 4RPM HXC 0.005252 0.4536 4.37158
7 3WMX THR 0.04133 0.40925 4.37158
8 2HCJ GDP 0.0153 0.42428 4.91803
9 3U6B GDP 0.01989 0.4183 4.91803
10 4B47 GDP 0.02944 0.40933 4.91803
11 1TL2 NDG 0.03694 0.40802 4.91803
12 4XFR CIT 0.03474 0.41278 5.15223
13 4CC6 L5Y 0.01166 0.43047 6.01093
14 4NOS ITU 0.04331 0.40045 6.55738
15 3KIF GDL 0.03176 0.41158 6.60377
16 1XE7 GUN 0.03122 0.42461 7.10383
17 4YMU ARG 0.04047 0.40336 7.10383
18 1WRA PC 0.03925 0.40583 7.65027
19 5C2N NAG 0.02113 0.42231 8.33333
20 4U60 SIA 0.02158 0.42181 9.28962
21 4U60 SIA GAL BGC NGA GAL 0.01984 0.41836 9.28962
22 4U60 SIA GAL NGA 0.03651 0.40206 9.28962
23 1TV5 ORO 0.03083 0.41335 9.83607
24 5H2U 1N1 0.02348 0.40023 9.83607
25 2WBV SIA 0.02217 0.41391 10.3825
26 3W68 4PT 0.04058 0.4001 11.4754
27 3WY9 GDP 0.02469 0.41337 12.5683
Pocket No.: 2; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3JVH; Ligand: HHV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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