Receptor
PDB id Resolution Class Description Source Keywords
3KO7 2.21 Å EC: 3.1.-.- DTD FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-LYSINE PLASMODIUM FALCIPARUM DTD DEACYLASE D-AMINO ACID D-LYSINE HYDROLASE
Ref.: LIGAND-BOUND STRUCTURES PROVIDE ATOMIC SNAPSHOTS FO CATALYTIC MECHANISM OF D-AMINO ACID DEACYLASE J.BIOL.CHEM. V. 285 5917 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DLY C:165;
Valid;
none;
submit data
146.188 C6 H14 N2 O2 C(CCN...
View in 3D viewer
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: DLY; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 DLY 1 1
2 ORN 0.714286 0.961538
3 2YG 0.609756 0.742857
4 API 0.607143 0.758621
5 DHH 0.59375 0.733333
6 LYS 0.59375 0.962963
7 2YJ 0.585366 0.742857
8 NPI 0.575758 0.733333
9 DAB 0.571429 0.857143
10 8SZ 0.542857 0.6
11 NLE 0.53125 0.7
12 MLZ 0.527778 0.787879
13 MLY 0.527778 0.657895
14 5CT 0.52381 0.764706
15 UN1 0.515152 0.7
16 11C 0.515152 0.7
17 0TF 0.511628 0.742857
18 ALY 0.487179 0.764706
19 HRG 0.487179 0.787879
20 ONH 0.485714 0.714286
21 NOT 0.475 0.735294
22 EXY 0.475 0.638889
23 26P 0.472222 0.636364
24 6CL 0.472222 0.733333
25 HSE 0.466667 0.709677
26 2YH 0.465116 0.735294
27 2RA 0.464286 0.758621
28 CIR 0.459459 0.714286
29 NVA 0.451613 0.689655
30 HCS 0.451613 0.785714
31 ARG 0.447368 0.735294
32 DAR 0.447368 0.735294
33 2NP 0.447368 0.628571
34 LBY 0.434783 0.619048
35 REZ 0.431818 0.638889
36 MSE 0.428571 0.617647
37 DGN 0.424242 0.65625
38 GLN 0.424242 0.65625
39 GGL 0.424242 0.666667
40 DGL 0.424242 0.666667
41 GLU 0.424242 0.666667
42 ILO 0.414634 0.735294
43 DSN 0.413793 0.666667
44 ABA 0.413793 0.642857
45 DBB 0.413793 0.642857
46 SER 0.413793 0.666667
47 SHR 0.413043 0.83871
48 DDW 0.410256 0.733333
49 DDK 0.410256 0.709677
50 CUW 0.405405 0.806452
51 9YT 0.405405 0.666667
52 C2N 0.4 0.678571
53 DCY 0.4 0.714286
54 ONL 0.4 0.606061
55 CYS 0.4 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: DLY; Similar ligands found: 319
No: Ligand Similarity coefficient
1 AKG 0.9739
2 3OL 0.9674
3 7C3 0.9673
4 9ON 0.9667
5 AG2 0.9647
6 MET 0.9610
7 2CO 0.9572
8 SLZ 0.9564
9 OGA 0.9558
10 LYN 0.9552
11 OOG 0.9522
12 KMT 0.9509
13 2HG 0.9482
14 NMH 0.9480
15 3OM 0.9446
16 BNF 0.9436
17 ACA 0.9420
18 HGA 0.9420
19 S2G 0.9411
20 SHV 0.9407
21 MED 0.9393
22 7OD 0.9376
23 O45 0.9374
24 M3P 0.9365
25 MHN 0.9365
26 2IT 0.9349
27 OCA 0.9338
28 5XA 0.9336
29 NYL 0.9321
30 N6C 0.9315
31 NWH 0.9314
32 3PG 0.9308
33 N4B 0.9307
34 LT1 0.9289
35 KQY 0.9288
36 DIR 0.9277
37 FXY 0.9273
38 MD0 0.9265
39 TIH 0.9265
40 HCI 0.9264
41 HPN 0.9256
42 BHH 0.9246
43 PBA 0.9236
44 PBN 0.9233
45 KDG 0.9230
46 PRA 0.9224
47 DZA 0.9223
48 0L1 0.9220
49 GGB 0.9220
50 S8V 0.9217
51 268 0.9209
52 HL5 0.9208
53 GUA 0.9206
54 650 0.9202
55 G3P 0.9197
56 MHO 0.9188
57 SYM 0.9186
58 HIS 0.9181
59 HTX 0.9174
60 13P 0.9173
61 264 0.9173
62 3LR 0.9173
63 2FM 0.9171
64 PEA 0.9167
65 LEU 0.9166
66 SME 0.9160
67 MPJ 0.9156
68 OEG 0.9156
69 ZGL 0.9155
70 ISZ 0.9153
71 258 0.9152
72 GJZ 0.9150
73 PO6 0.9149
74 PML 0.9147
75 CXP 0.9146
76 PGH 0.9144
77 URO 0.9144
78 YPN 0.9139
79 FK8 0.9136
80 AL0 0.9129
81 CXF 0.9128
82 HL4 0.9127
83 URQ 0.9124
84 DHI 0.9121
85 SKJ 0.9119
86 NTU 0.9118
87 263 0.9117
88 MXN 0.9115
89 49F 0.9112
90 SEP 0.9111
91 9J3 0.9109
92 SSB 0.9109
93 HG3 0.9108
94 NNH 0.9106
95 MNN 0.9103
96 7BC 0.9102
97 E4P 0.9097
98 IAR 0.9094
99 6NA 0.9094
100 I38 0.9093
101 DE5 0.9090
102 PZI 0.9088
103 NLP 0.9087
104 RAT 0.9087
105 CFI 0.9085
106 GP9 0.9074
107 PHE 0.9074
108 3H2 0.9067
109 4TB 0.9067
110 DAL DAL 0.9066
111 GLY GLY 0.9063
112 OSE 0.9062
113 1N5 0.9059
114 GPF 0.9057
115 1GP 0.9056
116 F06 0.9054
117 B40 0.9054
118 1DJ 0.9051
119 LY0 0.9047
120 MPH 0.9046
121 8GL 0.9044
122 SRT 0.9043
123 IVL 0.9042
124 I1E 0.9041
125 G3H 0.9035
126 GRQ 0.9032
127 KMH 0.9031
128 FAN 0.9031
129 CLT 0.9031
130 IP8 0.9029
131 HPV 0.9028
132 URP 0.9024
133 6XA 0.9016
134 E79 0.9016
135 ILE 0.9015
136 GPJ 0.9013
137 PG0 0.9010
138 SD4 0.9008
139 BHU 0.9008
140 IXW 0.9006
141 MUC 0.9005
142 SPV 0.9003
143 6JN 0.8998
144 K6V 0.8998
145 OKG 0.8995
146 2D8 0.8994
147 JX7 0.8989
148 AT3 0.8988
149 LTL 0.8987
150 OCT 0.8980
151 HFA 0.8979
152 MLT 0.8978
153 0VT 0.8974
154 XLS 0.8973
155 ENW 0.8971
156 ASP 0.8969
157 MF3 0.8964
158 SOR 0.8964
159 M4T 0.8964
160 MTL 0.8963
161 HHI 0.8951
162 B3U 0.8951
163 6HN 0.8950
164 011 0.8948
165 ENV 0.8947
166 64Z 0.8947
167 3MV 0.8944
168 DXG 0.8944
169 AHN 0.8943
170 DI6 0.8942
171 XYL 0.8940
172 3QM 0.8940
173 7UC 0.8939
174 2EH 0.8937
175 B3M 0.8936
176 HY1 0.8936
177 1SH 0.8933
178 BHL 0.8931
179 2JJ 0.8930
180 16D 0.8930
181 HOC 0.8925
182 R2P 0.8923
183 AX3 0.8922
184 NSD 0.8919
185 ALA ALA 0.8916
186 5XB 0.8915
187 3HG 0.8914
188 OHJ 0.8914
189 MEQ 0.8909
190 Q9Z 0.8909
191 3YP 0.8908
192 129 0.8905
193 VKC 0.8901
194 CCE 0.8898
195 NFA 0.8894
196 DPN 0.8892
197 XUL 0.8889
198 COI 0.8887
199 RTK 0.8885
200 AE3 0.8884
201 SKG 0.8883
202 DLT 0.8882
203 ASN 0.8875
204 1H1 0.8874
205 PJL 0.8873
206 CHH 0.8871
207 DHM 0.8871
208 CSS 0.8868
209 TLA 0.8867
210 GVA 0.8867
211 SHO 0.8867
212 LMR 0.8866
213 4TP 0.8866
214 SOL 0.8862
215 LPK 0.8859
216 F98 0.8855
217 RJY 0.8854
218 RNS 0.8853
219 HHH 0.8853
220 X1R 0.8853
221 GLY ALA 0.8851
222 TAR 0.8851
223 4LR 0.8848
224 XRG 0.8847
225 OC9 0.8842
226 CYX 0.8841
227 CCD 0.8839
228 DAV 0.8834
229 M1T 0.8833
230 LUQ 0.8832
231 HF2 0.8832
232 2FT 0.8827
233 7XA 0.8825
234 GLO 0.8824
235 AHL 0.8824
236 VAH 0.8823
237 41K 0.8822
238 FOM 0.8821
239 8EW 0.8821
240 KNA 0.8820
241 FOC 0.8816
242 R9M 0.8816
243 PAH 0.8814
244 DXP 0.8811
245 HBU 0.8808
246 HE4 0.8804
247 Q07 0.8802
248 TPO 0.8800
249 3S5 0.8793
250 GOJ 0.8792
251 ROR 0.8792
252 5FX 0.8789
253 2HC 0.8788
254 LNO 0.8785
255 AJ3 0.8784
256 C5A 0.8781
257 ZZU 0.8779
258 SPD 0.8778
259 EV0 0.8774
260 RBL 0.8773
261 OYA 0.8771
262 KPC 0.8771
263 MEV 0.8771
264 KOJ 0.8771
265 CS2 0.8764
266 OPE 0.8758
267 DAS 0.8758
268 HPL 0.8755
269 RUJ 0.8754
270 DEZ 0.8752
271 FUD 0.8752
272 K6H 0.8751
273 9GB 0.8750
274 1X4 0.8750
275 PRO GLY 0.8746
276 DYT 0.8745
277 LX1 0.8743
278 MAH 0.8743
279 152 0.8742
280 H7Y 0.8741
281 GVM 0.8740
282 SR1 0.8737
283 MLE 0.8729
284 DER 0.8721
285 HIC 0.8719
286 PC 0.8718
287 RB5 0.8717
288 PSJ 0.8716
289 98J 0.8714
290 THE 0.8701
291 MWP 0.8699
292 TEO 0.8690
293 NM3 0.8689
294 6Q3 0.8685
295 9X6 0.8683
296 XYH 0.8682
297 R67 0.8681
298 HPO 0.8678
299 QDK 0.8676
300 9SE 0.8675
301 1HS 0.8661
302 4WK 0.8659
303 4XR 0.8658
304 HDL 0.8650
305 JZ7 0.8645
306 RNT 0.8640
307 ACH 0.8637
308 3GZ 0.8637
309 LFC 0.8635
310 L06 0.8628
311 TAG 0.8627
312 DPF 0.8621
313 4ZD 0.8617
314 EHM 0.8611
315 5OY 0.8595
316 DII 0.8594
317 JFJ 0.8574
318 SDD 0.8567
319 ICF 0.8554
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
APoc FAQ
Feedback