Receptor
PDB id Resolution Class Description Source Keywords
3K2X 1.85 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSP SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI IN COMPLEX WITH 5'-C YTOSINE BURKHOLDERIA PSEUDOMALLEI NIAID SSGCID SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTDISEASE FRAGMENT-BASED DRUG DESIGN FBDD FRAGMENT CRYSTALISOPRENE BIOSYNTHESIS LYASE METAL-BINDING FRAGMENTS OF L
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:165;
Invalid;
none;
submit data
35.453 Cl [Cl-]
I5A A:164;
B:164;
C:164;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
353.114 C9 H12 I N3 O4 C1=CN...
K A:166;
Invalid;
none;
submit data
39.098 K [K+]
ZN A:163;
B:163;
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 (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: I5A; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 I5A 1 1
2 CTN 0.754717 0.920635
3 AR3 0.754717 0.920635
4 C 0.634921 0.828571
5 C5P 0.634921 0.828571
6 CAR 0.634921 0.828571
7 CDP 0.602941 0.816901
8 CTP 0.577465 0.816901
9 DKZ 0.571429 0.820895
10 CDP MG 0.571429 0.805556
11 7XL 0.546667 0.794521
12 C3P 0.545455 0.788732
13 C2G 0.525641 0.805556
14 CDC 0.5 0.716049
15 C2P 0.5 0.777778
16 C C 0.5 0.828571
17 CDM 0.493976 0.753247
18 C5G 0.488095 0.794521
19 CXY 0.482353 0.794521
20 V12 0.482353 0.794521
21 DCZ 0.46875 0.835821
22 LDC 0.46875 0.835821
23 NVG 0.454545 0.773333
24 GEO 0.454545 0.835821
25 CC7 0.445946 0.788732
26 1AA 0.44086 0.763158
27 CSV 0.43956 0.783784
28 CSQ 0.43956 0.783784
29 91P 0.421569 0.698795
30 PMT 0.405941 0.716049
31 LTT 0.402985 0.833333
32 DCM 0.4 0.743243
33 16B 0.4 0.77027
34 DC 0.4 0.743243
35 CTD 0.4 0.8125
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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