Receptor
PDB id Resolution Class Description Source Keywords
3IEW 2.1 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSP SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH BOUND CTP AND BURKHOLDERIA PSEUDOMALLEI ISPF STRUCTURAL GENOMICS ISOPRENE BIOSYNTHESIS LYASE METBINDING SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS SSGCID
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
CDP A:901;
C:901;
 Valid;
Valid;
 none;
none;
 submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
CTP B:901;
 Valid;
 none;
 submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
GOL B:163;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
ZN A:801;
B:801;
C:801;
 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 (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
2 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
3 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
4 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
5 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
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: CDP; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 HF4 0.895522 1
3 CTP 0.895522 1
4 CAR 0.787879 0.985507
5 C 0.787879 0.985507
6 C5P 0.787879 0.985507
7 7XL 0.77027 0.944444
8 0RC 0.77027 0.918919
9 2TM 0.743243 0.958333
10 C2G 0.74026 0.957747
11 CDC 0.725 0.82716
12 CDP MG 0.722222 0.942857
13 C5G 0.707317 0.944444
14 CDM 0.695122 0.894737
15 CXY 0.678571 0.944444
16 AR3 0.636364 0.857143
17 CTN 0.636364 0.857143
18 1AA 0.619565 0.906667
19 A7R 0.606383 0.931507
20 UDP 0.605263 0.942029
21 I5A 0.602941 0.816901
22 YYY 0.582278 0.90411
23 CDP RB0 0.577778 0.917808
24 GCQ 0.560976 0.90411
25 C3P 0.56 0.942857
26 MCN 0.557692 0.819277
27 PMT 0.554455 0.85
28 91P 0.553398 0.851852
29 UTP 0.54321 0.942029
30 2AA 0.542857 0.693878
31 16B 0.538462 0.917808
32 CSV 0.536842 0.905405
33 CSQ 0.536842 0.905405
34 U5F 0.536585 0.942029
35 DCP 0.535714 0.90411
36 GTF 0.523256 0.90411
37 C2P 0.519481 0.957143
38 PCD 0.517857 0.781609
39 FZQ 0.511364 0.797619
40 FN5 0.509434 0.871795
41 GPC 0.509091 0.819277
42 CSF 0.504587 0.871795
43 DKZ 0.5 0.746667
44 NCC 0.495413 0.918919
45 HQ5 0.48913 0.758621
46 UNP 0.488372 0.915493
47 DCT 0.488372 0.90411
48 TKW 0.4875 0.971429
49 G G 6MZ C 0.486239 0.814815
50 G C 0.481818 0.8375
51 5GW 0.477778 0.890411
52 5HM 0.47561 0.958333
53 BUP 0.471264 0.878378
54 YSC 0.469388 0.767442
55 DCM 0.463415 0.890411
56 DC 0.463415 0.890411
57 UPP 0.451613 0.888889
58 UDH 0.451613 0.844156
59 G8D 0.450549 0.907895
60 U 0.45 0.927536
61 U5P 0.45 0.927536
62 C5P SIA 0.447368 0.893333
63 660 0.446809 0.876712
64 UFM 0.446809 0.888889
65 GDU 0.446809 0.888889
66 URM 0.446809 0.876712
67 UPG 0.446809 0.888889
68 8OD 0.445652 0.855263
69 0KX 0.444444 0.88
70 UPU 0.444444 0.887324
71 4GW 0.443299 0.866667
72 DOC 0.439024 0.890411
73 M7G 0.43617 0.829268
74 U2F 0.43299 0.842105
75 UFG 0.43299 0.842105
76 UPF 0.43299 0.842105
77 2KH 0.431818 0.915493
78 AWU 0.427083 0.888889
79 CG2 0.421053 0.873418
80 G3N 0.42 0.890411
81 UDP UDP 0.418605 0.885714
82 UDX 0.418367 0.888889
83 UAD 0.418367 0.888889
84 44P 0.416667 0.902778
85 3UC 0.415842 0.842105
86 DCP MG 0.413043 0.851351
87 M7M 0.412371 0.797619
88 8GT 0.410526 0.907895
89 V12 0.41 0.75
90 UGB 0.41 0.901408
91 UGA 0.41 0.901408
92 USQ 0.41 0.780488
93 UGF 0.405941 0.853333
94 UP5 0.405405 0.857143
95 GEO 0.405063 0.783784
96 UDM 0.403846 0.864865
97 H6Y 0.402062 0.855263
98 NVG 0.401961 0.731707
99 CTP C C C C 0.4 0.915493
100 6MZ C U 0.4 0.814815
Ligand no: 2; Ligand: CTP; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 HF4 1 1
2 CTP 1 1
3 CDP 0.895522 1
4 C5P 0.753623 0.985507
5 CAR 0.753623 0.985507
6 C 0.753623 0.985507
7 0RC 0.74026 0.918919
8 7XL 0.74026 0.944444
9 C2G 0.734177 0.957747
10 2TM 0.714286 0.958333
11 C5G 0.702381 0.944444
12 CDM 0.690476 0.894737
13 CDC 0.678571 0.82716
14 CXY 0.674419 0.944444
15 CDP MG 0.671053 0.942857
16 UTP 0.620253 0.942029
17 1AA 0.617021 0.906667
18 U5F 0.6125 0.942029
19 DCP 0.609756 0.90411
20 CTN 0.608696 0.857143
21 AR3 0.608696 0.857143
22 A7R 0.604167 0.931507
23 GTF 0.595238 0.90411
24 91P 0.582524 0.851852
25 I5A 0.577465 0.816901
26 DCT 0.559524 0.90411
27 UDP 0.54321 0.942029
28 CDP RB0 0.542553 0.917808
29 2AA 0.542056 0.693878
30 MCN 0.542056 0.819277
31 BUP 0.541176 0.878378
32 C3P 0.538462 0.942857
33 YYY 0.52381 0.90411
34 PMT 0.52381 0.85
35 GCQ 0.523256 0.90411
36 CSQ 0.520408 0.905405
37 CSV 0.520408 0.905405
38 16B 0.518519 0.917808
39 PCD 0.517544 0.781609
40 FZQ 0.511111 0.797619
41 C2P 0.5 0.957143
42 GPC 0.495575 0.819277
43 FN5 0.495413 0.871795
44 CSF 0.491071 0.871795
45 NCC 0.482143 0.918919
46 DKZ 0.481013 0.746667
47 HQ5 0.473684 0.758621
48 8GT 0.473118 0.907895
49 UNP 0.47191 0.915493
50 TKW 0.46988 0.971429
51 H6Y 0.463158 0.855263
52 G G 6MZ C 0.460177 0.814815
53 5HM 0.458824 0.958333
54 G C 0.45614 0.8375
55 YSC 0.455446 0.767442
56 MGT 0.453608 0.829268
57 UDH 0.452632 0.844156
58 UPP 0.452632 0.888889
59 GDU 0.447917 0.888889
60 UFM 0.447917 0.888889
61 UPG 0.447917 0.888889
62 DCM 0.447059 0.890411
63 DC 0.447059 0.890411
64 UFG 0.434343 0.842105
65 UPF 0.434343 0.842105
66 U2F 0.434343 0.842105
67 U 0.433735 0.927536
68 U5P 0.433735 0.927536
69 URM 0.43299 0.876712
70 660 0.43299 0.876712
71 UP5 0.432432 0.857143
72 5GW 0.431579 0.890411
73 0KX 0.430108 0.88
74 UPU 0.430108 0.887324
75 AWU 0.428571 0.888889
76 PRT 0.424528 0.842105
77 C5P SIA 0.423729 0.893333
78 DOC 0.423529 0.890411
79 G3N 0.421569 0.890411
80 G8D 0.421053 0.907895
81 UDX 0.42 0.888889
82 UAD 0.42 0.888889
83 2KH 0.417582 0.915493
84 3UC 0.417476 0.842105
85 4GW 0.415842 0.866667
86 UGA 0.411765 0.901408
87 UGB 0.411765 0.901408
88 USQ 0.411765 0.780488
89 V12 0.411765 0.75
90 CG2 0.410256 0.873418
91 UGF 0.407767 0.853333
92 GEO 0.407407 0.783784
93 NVG 0.403846 0.731707
94 44P 0.402299 0.902778
95 8OD 0.402062 0.855263
Similar Ligands (3D)
Ligand no: 1; Ligand: CDP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DUD 0.9790
2 TBD 0.9634
3 TYD 0.9611
4 ADP 0.9333
5 D4D 0.9313
6 DUN 0.9274
7 ADX 0.9253
8 IDP 0.9252
9 BEF ADP 0.9235
10 AU1 0.9225
11 AN2 0.9215
12 ADP MG 0.9194
13 UMP 0.9193
14 AP2 0.9182
15 A12 0.9182
16 DGI 0.9158
17 M33 0.9122
18 CUU 0.9102
19 GDP 0.9093
20 AMP 0.9080
21 U3S 0.9071
22 DAT 0.9016
23 TMP 0.8942
24 U1S 0.8914
25 CH 0.8874
26 H2U 0.8816
27 2A5 0.8762
28 DU 0.8746
29 SON 0.8726
30 SSA 0.8707
31 AZD 0.8684
32 7D3 0.8672
33 T3S 0.8656
34 DDN 0.8643
35 DUT 0.8631
36 AMZ 0.8619
37 C8M 0.8613
38 BMP 0.8569
Ligand no: 2; Ligand: CTP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DCP MG 0.9768
2 ATP 0.9340
3 ANP 0.9332
4 BEF ADP 0.9306
5 DTP 0.9261
6 AGS 0.9211
7 GNP 0.9164
8 GTP 0.9139
9 GSP 0.9100
10 523 0.9081
11 DUT 0.9057
12 ADP ALF 0.9037
13 BEF GDP 0.9014
14 GCP 0.9014
15 ACP 0.9009
16 9GM 0.8976
17 TTP 0.8971
18 GDP BEF 0.8953
19 DBG 0.8952
20 GDP AF3 0.8952
21 ALF GDP 0.8897
22 APC 0.8893
23 GDP ALF 0.8876
24 3AT 0.8869
25 ADP BEF 0.8816
26 DUP 0.8797
27 ALF ADP 0.8743
28 GH3 0.8739
29 VO4 ADP 0.8731
30 D3T 0.8678
31 TYD 0.8658
32 DGT 0.8611
33 ADP AF3 0.8574
34 SFG 0.8566
35 D4T 0.8549
36 AD9 0.8544
37 SAM 0.8538
38 TLO 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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