Receptor
PDB id Resolution Class Description Source Keywords
3IEQ 2.1 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSP SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH CYTIDINE BURKHOLDERIA PSEUDOMALLEI NIAID ISOPRENE BIOSYNTHESIS LYASE METAL-BINDING STRUCTURGENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUSSSGCID
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
C A:901;
B:901;
C:901;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
323.197 C9 H14 N3 O8 P C1=CN...
CL A:164;
Invalid;
none;
submit data
35.453 Cl [Cl-]
MG B:163;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
ZN A:163;
B:164;
C:163;
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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
3 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
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: C; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 C 1 1
2 CAR 1 1
3 C5P 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 CDP MG 0.724638 0.916667
7 7XL 0.689189 0.930556
8 16B 0.676471 0.930556
9 AR3 0.672131 0.842857
10 CTN 0.672131 0.842857
11 C2G 0.662338 0.943662
12 I5A 0.634921 0.828571
13 C5G 0.634146 0.930556
14 C C 0.632911 0.942857
15 CDC 0.62963 0.8375
16 CDM 0.621951 0.881579
17 CXY 0.607143 0.930556
18 TKW 0.591549 0.985507
19 C3P 0.585714 0.956522
20 5HM 0.575342 0.944444
21 U5P 0.571429 0.941176
22 CSV 0.555556 0.917808
23 CSQ 0.555556 0.917808
24 1AA 0.554348 0.893333
25 C2P 0.541667 0.942857
26 PMT 0.540816 0.860759
27 DCM 0.540541 0.902778
28 DC 0.540541 0.902778
29 DKZ 0.521127 0.733333
30 91P 0.495146 0.839506
31 FN5 0.495146 0.858974
32 DOC 0.493333 0.902778
33 ICR 0.486842 0.861111
34 5BU 0.486842 0.876712
35 2AA 0.485714 0.683673
36 MCN 0.485714 0.807229
37 GPC 0.481481 0.829268
38 G C 0.481132 0.848101
39 5FU 0.48 0.876712
40 CSF 0.476636 0.858974
41 PCD 0.464286 0.770115
42 U A C C 0.463636 0.857143
43 C5P SIA 0.458716 0.88
44 YYY 0.451219 0.890411
45 CNU 0.45 0.915493
46 UDP 0.45 0.927536
47 44P 0.448718 0.888889
48 DCP 0.447059 0.890411
49 G G G C 0.442478 0.860759
50 A G C C 0.438596 0.858974
51 V12 0.43617 0.7375
52 NUP 0.435897 0.929577
53 GCQ 0.435294 0.890411
54 UTP 0.433735 0.927536
55 A U C C 0.429752 0.846154
56 2KH 0.428571 0.901408
57 UP6 0.428571 0.887324
58 NVG 0.427083 0.719512
59 G C C C 0.423729 0.871795
60 S5P 0.423077 0.853333
61 GEO 0.418919 0.77027
62 CH 0.417722 0.956522
63 H2U 0.415584 0.861111
64 UDP UDP 0.414634 0.898551
65 FNU 0.4125 0.88
66 JW5 0.4125 0.901408
67 8GM 0.411765 0.906667
68 DCZ 0.410959 0.77027
69 LDC 0.410959 0.77027
70 UPU 0.409091 0.9
71 BMP 0.405063 0.901408
72 BMQ 0.402597 0.885714
73 UNP 0.402299 0.901408
74 8OP 0.402299 0.853333
75 U6M 0.4 0.914286
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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