Receptor
PDB id Resolution Class Description Source Keywords
4NBJ 2.2 Å EC: 3.1.-.- D-AMINOACYL-TRNA DEACYLASE (DTD) FROM PLASMODIUM FALCIPARUM WITH D-TYROSYL-3'-AMINOADENOSINE AT 2.20 ANGSTROM RESOLUTIO PLASMODIUM FALCIPARUM DTD DEACYLASE DTD-LIKE HYDROLASE
Ref.: MECHANISM OF CHIRAL PROOFREADING DURING TRANSLATION GENETIC CODE. ELIFE V. 2 01519 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D3Y B:201;
A:201;
H:201;
E:201;
C:201;
D:201;
F:201;
G:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
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429.43 C19 H23 N7 O5 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4NBI 1.86 Å EC: 3.1.-.- D-AMINOACYL-TRNA DEACYLASE (DTD) FROM PLASMODIUM FALCIPARUM WITH D-TYROSYL-3'-AMINOADENOSINE AT 1.86 ANGSTROM RESOLUTIO PLASMODIUM FALCIPARUM DTD DEACYLASE DTD-LIKE HYDROLASE
Ref.: MECHANISM OF CHIRAL PROOFREADING DURING TRANSLATION GENETIC CODE. ELIFE V. 2 01519 2013
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 3KO5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 4NBI - D3Y C19 H23 N7 O5 c1cc(ccc1C....
3 3KO7 - DLY C6 H14 N2 O2 C(CCN)C[C@....
4 5J61 - A3G C12 H17 N7 O4 c1nc(c2c(n....
5 4NBJ - D3Y C19 H23 N7 O5 c1cc(ccc1C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 3KO5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 4NBI - D3Y C19 H23 N7 O5 c1cc(ccc1C....
3 3KO7 - DLY C6 H14 N2 O2 C(CCN)C[C@....
4 5J61 - A3G C12 H17 N7 O4 c1nc(c2c(n....
5 4NBJ - D3Y C19 H23 N7 O5 c1cc(ccc1C....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3KO5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 4NBI - D3Y C19 H23 N7 O5 c1cc(ccc1C....
3 3KO7 - DLY C6 H14 N2 O2 C(CCN)C[C@....
4 5J61 - A3G C12 H17 N7 O4 c1nc(c2c(n....
5 4NBJ - D3Y C19 H23 N7 O5 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: D3Y; Similar ligands found: 140
No: Ligand ECFP6 Tc MDL keys Tc
1 D3Y 1 1
2 3NZ 0.827586 0.956522
3 A3S 0.743902 0.969697
4 A3T 0.666667 0.925373
5 A3G 0.623529 0.955224
6 YSA 0.607843 0.752941
7 J4G 0.574257 0.794872
8 VRT 0.510204 0.914286
9 5X8 0.494845 0.884058
10 2VA 0.494845 0.898551
11 SO8 0.48 0.885714
12 RAB 0.47619 0.924242
13 ADN 0.47619 0.924242
14 XYA 0.47619 0.924242
15 6RE 0.473118 0.824324
16 NVA 2AD 0.47 0.901408
17 5N5 0.465116 0.895522
18 SFG 0.464646 0.869565
19 A4D 0.45977 0.895522
20 NWW 0.45977 0.833333
21 5CD 0.45977 0.852941
22 M2T 0.455556 0.773333
23 FA5 0.455357 0.828947
24 GLU GMC 0.45283 0.853333
25 3AM 0.451613 0.773333
26 J7C 0.447917 0.835616
27 SSA 0.447619 0.752941
28 S7M 0.447619 0.792208
29 7D7 0.447059 0.811594
30 A 0.446809 0.786667
31 AMP 0.446809 0.786667
32 SAM 0.446602 0.792208
33 LSS 0.444444 0.696629
34 0UM 0.444444 0.826667
35 GJV 0.443299 0.813333
36 EEM 0.442308 0.792208
37 FYA 0.441441 0.826667
38 SA8 0.441176 0.813333
39 AHX 0.440367 0.820513
40 DTA 0.43956 0.830986
41 5CA 0.439252 0.752941
42 A3P 0.438776 0.763158
43 A5A 0.438095 0.697674
44 KB1 0.4375 0.826667
45 NEC 0.4375 0.84058
46 N5O 0.4375 0.911765
47 SAI 0.436893 0.847222
48 SAH 0.436893 0.859155
49 5AD 0.435294 0.791045
50 SRP 0.433962 0.828947
51 SMM 0.433962 0.7625
52 GSU 0.432432 0.712644
53 DSZ 0.431193 0.732558
54 7D5 0.430108 0.730769
55 SON 0.43 0.782051
56 54H 0.429907 0.681818
57 VMS 0.429907 0.681818
58 N5A 0.428571 0.882353
59 NB8 0.428571 0.797468
60 EP4 0.428571 0.794521
61 5AL 0.428571 0.779221
62 DLL 0.427273 0.802632
63 AMP MG 0.427083 0.797297
64 QA7 0.425926 0.75
65 TSB 0.425926 0.709302
66 53H 0.425926 0.674157
67 CA0 0.425743 0.792208
68 3DH 0.425532 0.816901
69 NWQ 0.425532 0.808824
70 KG4 0.421569 0.792208
71 WSA 0.421488 0.741176
72 HZ2 0.420168 0.890411
73 ADP 0.42 0.789474
74 R2V 0.419643 0.759036
75 KAA 0.419643 0.707865
76 MTA 0.419355 0.816901
77 ABM 0.418367 0.766234
78 A3N 0.418367 0.857143
79 45A 0.418367 0.766234
80 A2D 0.418367 0.813333
81 AMO 0.418182 0.828947
82 ZAS 0.416667 0.808219
83 52H 0.416667 0.674157
84 LMS 0.416667 0.694118
85 AN2 0.415842 0.779221
86 Y3J 0.41573 0.768116
87 7MD 0.415254 0.790123
88 V2G 0.415094 0.775
89 S4M 0.414141 0.7625
90 KYE 0.413793 0.794872
91 XAH 0.413793 0.768293
92 PAP 0.413462 0.776316
93 HY8 0.413223 0.890411
94 8LQ 0.412844 0.782051
95 OVE 0.412371 0.75641
96 SRA 0.412371 0.746835
97 MHZ 0.411765 0.753086
98 AU1 0.411765 0.769231
99 2AM 0.410526 0.786667
100 BA3 0.41 0.813333
101 A12 0.41 0.782051
102 AP2 0.41 0.782051
103 G5A 0.409524 0.732558
104 8QN 0.409091 0.779221
105 9ZA 0.409091 0.740741
106 9ZD 0.409091 0.740741
107 AOC 0.408163 0.842857
108 ACP 0.407767 0.792208
109 HEJ 0.407767 0.789474
110 ATP 0.407767 0.789474
111 V47 0.407407 0.855072
112 8LH 0.407407 0.782051
113 WAQ 0.40708 0.7625
114 LAD 0.40708 0.7875
115 QQX 0.40625 0.708861
116 5AS 0.405941 0.674157
117 AP5 0.405941 0.813333
118 B4P 0.405941 0.813333
119 ACQ 0.40566 0.792208
120 GAP 0.40566 0.792208
121 PAJ 0.405405 0.765432
122 NSS 0.405405 0.732558
123 KL2 0.404255 0.736842
124 AQP 0.403846 0.789474
125 APC 0.403846 0.782051
126 5FA 0.403846 0.789474
127 ME8 0.403509 0.746988
128 QQY 0.402062 0.717949
129 ACK 0.402062 0.756757
130 AT4 0.401961 0.759494
131 ADP BEF 0.401961 0.786667
132 ADP MG 0.401961 0.786667
133 PPS 0.401869 0.694118
134 8LE 0.401869 0.75
135 62X 0.401786 0.7625
136 NVA LMS 0.401786 0.688889
137 KXW 0.4 0.863014
138 DAL AMP 0.4 0.779221
139 A5D 0.4 0.830986
140 7D3 0.4 0.734177
Similar Ligands (3D)
Ligand no: 1; Ligand: D3Y; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NBI; Ligand: D3Y; 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: 4nbi.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4NBI; Ligand: D3Y; 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: 4nbi.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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