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 (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: I5A; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 I5A 1 1
2 CTN 0.754717 0.920635
3 AR3 0.754717 0.920635
4 CAR 0.634921 0.828571
5 C5P 0.634921 0.828571
6 C 0.634921 0.828571
7 CDP 0.602941 0.816901
8 CDP MG 0.57971 0.84058
9 HF4 0.577465 0.816901
10 CTP 0.577465 0.816901
11 DKZ 0.571429 0.820895
12 0RC 0.546667 0.773333
13 7XL 0.546667 0.794521
14 C3P 0.545455 0.788732
15 2TM 0.540541 0.783784
16 C2G 0.525641 0.805556
17 FZQ 0.512821 0.690476
18 CDC 0.5 0.716049
19 C2P 0.5 0.777778
20 CDM 0.493976 0.753247
21 C5G 0.488095 0.794521
22 HQ5 0.487805 0.674419
23 V12 0.482353 0.794521
24 CXY 0.482353 0.794521
25 DCZ 0.46875 0.835821
26 LDC 0.46875 0.835821
27 CDP RB0 0.45977 0.794521
28 NVG 0.454545 0.773333
29 GEO 0.454545 0.835821
30 YSC 0.449438 0.682353
31 CC7 0.445946 0.788732
32 1AA 0.44086 0.763158
33 CSV 0.43956 0.783784
34 CSQ 0.43956 0.783784
35 A7R 0.431579 0.783784
36 91P 0.421569 0.698795
37 PMT 0.405941 0.716049
38 LTT 0.402985 0.833333
39 16B 0.4 0.77027
40 CTD 0.4 0.8125
41 DC 0.4 0.743243
42 DCM 0.4 0.743243
Similar Ligands (3D)
Ligand no: 1; Ligand: I5A; Similar ligands found: 184
No: Ligand Similarity coefficient
1 URI 0.9703
2 DUR 0.9671
3 URD 0.9560
4 TYU 0.9559
5 F01 0.9555
6 5AE 0.9543
7 PIR 0.9428
8 2TU 0.9427
9 THU 0.9419
10 UUA 0.9413
11 THM 0.9412
12 DDU 0.9375
13 ZEB 0.9341
14 5BT 0.9304
15 TBN 0.9267
16 0DN 0.9264
17 ADN 0.9253
18 IMH 0.9251
19 DHZ 0.9250
20 5UD 0.9249
21 TMC 0.9238
22 A 0.9229
23 NOS 0.9227
24 MCY 0.9216
25 FMB 0.9204
26 9DI 0.9204
27 UA2 0.9199
28 AD3 0.9193
29 HPR 0.9180
30 PRH 0.9180
31 FMC 0.9175
32 5MD 0.9175
33 TIA 0.9173
34 ID2 0.9158
35 K80 0.9151
36 TIZ 0.9139
37 5AD 0.9134
38 DBM 0.9091
39 B86 0.9091
40 TAL 0.9080
41 3D1 0.9076
42 MTA 0.9064
43 XYA 0.9058
44 BRD 0.9055
45 NNR 0.9053
46 3BH 0.9046
47 DNB 0.9037
48 MTP 0.9031
49 1KN 0.9022
50 5ID 0.9019
51 EKH 0.9016
52 5NB 0.9008
53 FTU 0.9001
54 SCT 0.9000
55 GMP 0.8998
56 ZYV 0.8994
57 9UL 0.8972
58 HNL 0.8971
59 QMR 0.8965
60 FT1 0.8948
61 AHU 0.8943
62 W29 0.8942
63 HNK 0.8924
64 3DT 0.8897
65 1Z6 0.8893
66 QBS 0.8892
67 B2T 0.8883
68 CC5 0.8879
69 A4Q 0.8878
70 M2T 0.8867
71 PF1 0.8865
72 PQT 0.8864
73 X11 0.8863
74 16Z 0.8863
75 46P 0.8852
76 FTV 0.8841
77 KTJ 0.8827
78 BP3 0.8827
79 50C 0.8824
80 L13 0.8823
81 N2Y 0.8813
82 U 0.8810
83 A6H 0.8810
84 U5P 0.8808
85 BPY 0.8804
86 M5E 0.8802
87 9W5 0.8801
88 AUV 0.8785
89 TCL 0.8774
90 S0G 0.8772
91 RFZ 0.8772
92 5VL 0.8764
93 FB4 0.8764
94 H2U 0.8764
95 1WC 0.8761
96 3Y7 0.8758
97 TYR 0.8758
98 N8M 0.8754
99 FCD 0.8749
100 6J9 0.8746
101 ANU 0.8741
102 B21 0.8741
103 A4N 0.8741
104 A9O 0.8739
105 6HX 0.8736
106 LLT 0.8732
107 EXR 0.8731
108 JRB 0.8728
109 HWD 0.8727
110 1CY 0.8725
111 TRP 0.8716
112 EN1 0.8716
113 TT4 0.8712
114 TI7 0.8711
115 EAJ 0.8709
116 7QV 0.8703
117 HNH 0.8699
118 VIB 0.8697
119 EAT 0.8694
120 FMQ 0.8692
121 A8Q 0.8690
122 PJW 0.8689
123 NCT 0.8689
124 ZIQ 0.8687
125 FC2 0.8681
126 MOK 0.8676
127 9FH 0.8675
128 WVV 0.8673
129 OA1 0.8672
130 B2Y 0.8671
131 22L 0.8669
132 WOE 0.8664
133 7R7 0.8662
134 JF8 0.8661
135 BP6 0.8657
136 X6P 0.8656
137 XIF XYP 0.8655
138 CH9 0.8653
139 CP6 0.8652
140 GNG 0.8649
141 A4T 0.8647
142 9FG 0.8647
143 F63 0.8639
144 MPK 0.8639
145 FN5 0.8638
146 XYP XIF 0.8638
147 UMP 0.8635
148 F6P 0.8633
149 89J 0.8625
150 8OE 0.8624
151 SV4 0.8624
152 78U 0.8624
153 1A7 0.8623
154 XK0 0.8621
155 1VK 0.8619
156 XDK 0.8615
157 3TC 0.8611
158 DTY 0.8609
159 54E 0.8608
160 MUK 0.8607
161 C53 0.8606
162 0OL 0.8605
163 8OB 0.8605
164 1XA 0.8604
165 DTR 0.8600
166 G14 0.8584
167 PFF 0.8580
168 C0H 0.8576
169 JZA 0.8573
170 YOF 0.8565
171 HNM 0.8560
172 X48 0.8559
173 Y4L 0.8556
174 XFE 0.8553
175 H7S 0.8552
176 BDJ 0.8547
177 DIF 0.8543
178 QUS 0.8535
179 TMP 0.8529
180 4I8 0.8509
181 AVA 0.8508
182 2GD 0.8506
183 51Y 0.8506
184 R9G 0.8505
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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