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Receptor
PDB id Resolution Class Description Source Keywords
3IID 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE MACRO DOMAIN OF HUMAN HISTONE MACRO COMPLEX WITH ADP-RIBOSE (FORM A) HOMO SAPIENS HISTONE CHROMATIN MACRO DOMAIN CHROMATIN REGULATOR CHROMPROTEIN DNA-BINDING ISOPEPTIDE BOND METHYLATION NUCLEOSNUCLEUS PHOSPHOPROTEIN GENE REGULATION
Ref.: A MACRODOMAIN-CONTAINING HISTONE REARRANGES CHROMAT SENSING PARP1 ACTIVATION. NAT.STRUCT.MOL.BIOL. V. 16 923 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
APR A:400;
Valid;
none;
submit data
559.316 C15 H23 N5 O14 P2 c1nc(...
NO3 A:401;
Invalid;
none;
submit data
62.005 N O3 [N+](...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3IID 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE MACRO DOMAIN OF HUMAN HISTONE MACRO COMPLEX WITH ADP-RIBOSE (FORM A) HOMO SAPIENS HISTONE CHROMATIN MACRO DOMAIN CHROMATIN REGULATOR CHROMPROTEIN DNA-BINDING ISOPEPTIDE BOND METHYLATION NUCLEOSNUCLEUS PHOSPHOPROTEIN GENE REGULATION
Ref.: A MACRODOMAIN-CONTAINING HISTONE REARRANGES CHROMAT SENSING PARP1 ACTIVATION. NAT.STRUCT.MOL.BIOL. V. 16 923 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3IID - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 3IIF - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3IID - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 3IIF - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3IID - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 3IIF - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: APR; Similar ligands found: 398
No: Ligand ECFP6 Tc MDL keys Tc
1 APR 1 1
2 AR6 1 1
3 A2D 0.898551 0.971831
4 BA3 0.847222 0.971831
5 B4P 0.835616 0.971831
6 AP5 0.835616 0.971831
7 M33 0.813333 0.958333
8 ADP 0.810811 0.971831
9 ADV 0.805195 0.958904
10 RBY 0.805195 0.958904
11 HEJ 0.802632 0.971831
12 ATP 0.802632 0.971831
13 AT4 0.8 0.932432
14 AN2 0.8 0.958333
15 5FA 0.792208 0.971831
16 AQP 0.792208 0.971831
17 AD9 0.782051 0.945205
18 AGS 0.782051 0.92
19 SAP 0.782051 0.92
20 ACP 0.779221 0.945205
21 A 0.753425 0.943662
22 AMP 0.753425 0.943662
23 3OD 0.747126 0.972222
24 PRX 0.746835 0.893333
25 9X8 0.744186 0.945946
26 OAD 0.744186 0.972222
27 CA0 0.74359 0.972222
28 ADX 0.74359 0.873418
29 ACQ 0.740741 0.945205
30 ANP 0.740741 0.945205
31 A22 0.738095 0.958333
32 50T 0.734177 0.931507
33 A2R 0.72619 0.985915
34 ABM 0.723684 0.917808
35 ATF 0.722892 0.932432
36 A1R 0.72093 0.907895
37 ADQ 0.72093 0.972222
38 A3R 0.72093 0.907895
39 6YZ 0.714286 0.945205
40 A12 0.705128 0.932432
41 AP2 0.705128 0.932432
42 SRA 0.697368 0.893333
43 5AL 0.690476 0.958333
44 APC 0.682927 0.932432
45 AU1 0.679012 0.945205
46 TAT 0.678571 0.932432
47 T99 0.678571 0.932432
48 SRP 0.674419 0.932432
49 BIS 0.67033 0.907895
50 25L 0.663043 0.958333
51 4AD 0.662921 0.945946
52 DLL 0.655556 0.958333
53 00A 0.655556 0.907895
54 ADP PO3 0.654762 0.943662
55 8QN 0.651685 0.958333
56 5SV 0.651685 0.848101
57 OOB 0.651685 0.958333
58 25A 0.651685 0.944444
59 DQV 0.649485 0.958333
60 PAJ 0.644444 0.909091
61 AMO 0.644444 0.958904
62 MAP 0.640449 0.92
63 OMR 0.64 0.875
64 AFH 0.639175 0.909091
65 AHX 0.637363 0.896104
66 FYA 0.634409 0.905405
67 3UK 0.630435 0.945205
68 NAX 0.63 0.873418
69 G3A 0.628866 0.896104
70 SON 0.626506 0.932432
71 ALF ADP 0.625 0.87013
72 ADP ALF 0.625 0.87013
73 B5V 0.623656 0.932432
74 PR8 0.623656 0.873418
75 WAQ 0.623656 0.907895
76 LAD 0.623656 0.884615
77 G5P 0.622449 0.896104
78 GAP 0.62069 0.918919
79 LMS 0.620253 0.82716
80 48N 0.62 0.921053
81 ADP VO4 0.617977 0.931507
82 VO4 ADP 0.617977 0.931507
83 AP0 0.617647 0.896104
84 ME8 0.617021 0.8625
85 TXA 0.617021 0.958904
86 PTJ 0.617021 0.896104
87 1ZZ 0.617021 0.8625
88 NB8 0.617021 0.921053
89 GTA 0.616162 0.8625
90 FA5 0.614583 0.932432
91 TXD 0.613861 0.907895
92 NAI 0.613861 0.907895
93 6V0 0.613861 0.896104
94 DND 0.613861 0.958904
95 NXX 0.613861 0.958904
96 TXE 0.607843 0.907895
97 DAL AMP 0.604396 0.931507
98 9SN 0.604167 0.896104
99 UP5 0.598039 0.92
100 YAP 0.597938 0.92
101 B5Y 0.597938 0.92
102 B5M 0.597938 0.92
103 9ZD 0.597826 0.907895
104 9ZA 0.597826 0.907895
105 XAH 0.591837 0.839506
106 RAB 0.589041 0.84507
107 ADN 0.589041 0.84507
108 XYA 0.589041 0.84507
109 2A5 0.586207 0.893333
110 4UV 0.585859 0.92
111 AOC 0.585366 0.821918
112 ADJ 0.584906 0.875
113 7D4 0.581395 0.88
114 ITT 0.581395 0.916667
115 A4P 0.580952 0.821429
116 ATR 0.579545 0.943662
117 PAP 0.579545 0.957747
118 CNA 0.579439 0.932432
119 ADP BMA 0.578947 0.945205
120 5AS 0.576471 0.77907
121 4UU 0.574257 0.92
122 GA7 0.574257 0.906667
123 F2R 0.574074 0.864198
124 5N5 0.573333 0.819444
125 7D3 0.571429 0.88
126 4TC 0.571429 0.896104
127 139 0.570093 0.873418
128 T5A 0.570093 0.841463
129 COD 0.568807 0.811765
130 JB6 0.56701 0.883117
131 A4D 0.565789 0.819444
132 5CD 0.565789 0.805556
133 EP4 0.564103 0.753247
134 LAQ 0.563107 0.8625
135 NA7 0.5625 0.932432
136 TYM 0.561905 0.932432
137 80F 0.558559 0.864198
138 YLP 0.557692 0.841463
139 A A 0.556701 0.917808
140 G5A 0.555556 0.77907
141 HFD 0.555556 0.92
142 4UW 0.552381 0.884615
143 ATP A A A 0.55 0.930556
144 AVV 0.547368 0.896104
145 A3P 0.546512 0.943662
146 MYR AMP 0.545455 0.839506
147 7D5 0.54321 0.853333
148 G1R 0.542553 0.907895
149 YLC 0.542056 0.8625
150 UPA 0.542056 0.907895
151 YLB 0.542056 0.841463
152 NAD 0.540541 0.931507
153 TYR AMP 0.539216 0.894737
154 AMP DBH 0.539216 0.918919
155 TAD 0.538462 0.884615
156 DTA 0.5375 0.786667
157 M2T 0.5375 0.734177
158 3DH 0.536585 0.773333
159 AYB 0.536364 0.831325
160 EAD 0.533898 0.873418
161 AHZ 0.533333 0.839506
162 FB0 0.532787 0.784091
163 IOT 0.53211 0.831325
164 A3D 0.530973 0.918919
165 MTA 0.530864 0.773333
166 3AM 0.53012 0.902778
167 ARG AMP 0.528846 0.829268
168 AR6 AR6 0.528846 0.944444
169 A2P 0.528736 0.929577
170 YLA 0.527273 0.841463
171 6AD 0.526882 0.884615
172 PPS 0.526882 0.85
173 BTX 0.526786 0.819277
174 NAE 0.525862 0.894737
175 BT5 0.522124 0.831325
176 A5A 0.521277 0.807229
177 TSB 0.520833 0.819277
178 6RE 0.517647 0.7375
179 P1H 0.516393 0.851852
180 3AT 0.516129 0.944444
181 SSA 0.515789 0.8
182 7MD 0.514286 0.886076
183 54H 0.510417 0.788235
184 52H 0.510417 0.77907
185 VMS 0.510417 0.788235
186 NSS 0.510204 0.8
187 NAQ 0.508475 0.871795
188 ZAS 0.505882 0.766234
189 IMO 0.505747 0.902778
190 J7C 0.505747 0.746835
191 A3N 0.505747 0.786667
192 AV2 0.505263 0.891892
193 R5I 0.505263 0.918919
194 R7I 0.505263 0.918919
195 53H 0.505155 0.77907
196 5CA 0.505155 0.8
197 8X1 0.505155 0.752809
198 ARU 0.50505 0.8375
199 NVA LMS 0.50505 0.752809
200 9K8 0.504951 0.733333
201 AF3 ADP 3PG 0.504587 0.860759
202 YLY 0.504274 0.831325
203 ZID 0.504202 0.918919
204 S4M 0.5 0.666667
205 V3L 0.5 0.971831
206 FDA 0.5 0.811765
207 LEU LMS 0.5 0.752809
208 DTP 0.5 0.88
209 LPA AMP 0.5 0.839506
210 2AM 0.5 0.916667
211 FNK 0.496183 0.784091
212 6FA 0.496063 0.841463
213 DZD 0.495652 0.884615
214 P5A 0.49505 0.744444
215 DSZ 0.494949 0.821429
216 LSS 0.494949 0.761364
217 MAO 0.494382 0.759036
218 DSH 0.494253 0.725
219 M24 0.491525 0.873418
220 NJP 0.491228 0.92
221 5X8 0.48913 0.786667
222 DAT 0.48913 0.88
223 SFD 0.488372 0.734043
224 FAS 0.488372 0.851852
225 FAD 0.488372 0.851852
226 NAJ PZO 0.487179 0.848101
227 0WD 0.486957 0.896104
228 NPW 0.486726 0.8625
229 7MC 0.486486 0.864198
230 7DT 0.483871 0.957747
231 7DD 0.483516 0.957747
232 GJV 0.483146 0.728395
233 OVE 0.482759 0.88
234 5AD 0.480519 0.746479
235 GSU 0.480392 0.8
236 KAA 0.480392 0.752809
237 NDE 0.48 0.906667
238 N0B 0.479339 0.841463
239 A5D 0.478723 0.786667
240 ODP 0.478261 0.884615
241 RGT 0.47619 0.958904
242 XNP 0.474138 0.85
243 4TA 0.474138 0.807229
244 AMP NAD 0.474138 0.931507
245 62F 0.473684 0.8625
246 NDP 0.473684 0.896104
247 SFG 0.473118 0.773333
248 NDC 0.472441 0.871795
249 YSA 0.471698 0.77907
250 NAJ PYZ 0.471074 0.807229
251 ENP 0.470588 0.918919
252 FAY 0.470149 0.8625
253 TXP 0.469565 0.896104
254 NZQ 0.469565 0.884615
255 DDS 0.46875 0.853333
256 A7D 0.467391 0.776316
257 RFL 0.466667 0.821429
258 ENQ 0.466019 0.943662
259 AAT 0.463918 0.707317
260 SA8 0.463158 0.728395
261 7C5 0.462963 0.818182
262 MHZ 0.462366 0.697674
263 8PZ 0.462264 0.8
264 71V 0.461538 0.883117
265 G A A A 0.461538 0.848101
266 F2N 0.460993 0.793103
267 NEC 0.460674 0.746667
268 A3G 0.460674 0.8
269 GGZ 0.46 0.825
270 6C6 0.458333 0.857143
271 SAH 0.458333 0.766234
272 SAI 0.458333 0.75641
273 P5F 0.457143 0.823529
274 Y3J 0.45679 0.726027
275 A A A 0.456311 0.905405
276 PO4 PO4 A A A A PO4 0.456311 0.902778
277 7D7 0.455696 0.743243
278 SMM 0.454545 0.705882
279 V1N 0.453704 0.944444
280 6IA 0.453608 0.814815
281 SAM 0.453608 0.710843
282 WSA 0.451327 0.788235
283 U A 0.45 0.883117
284 A G 0.449153 0.858974
285 EEM 0.44898 0.710843
286 PGS 0.446809 0.858974
287 ETB 0.446281 0.811765
288 DCA 0.446281 0.802326
289 U A G G 0.445378 0.858974
290 2SA 0.444444 0.932432
291 D5M 0.444444 0.853333
292 DA 0.444444 0.853333
293 GP3 0.443299 0.896104
294 9JJ 0.442857 0.8625
295 128 0.442478 0.776471
296 4YB 0.441441 0.781609
297 GEK 0.441176 0.759494
298 Z5A 0.44 0.77907
299 30N 0.44 0.734043
300 S7M 0.44 0.710843
301 AAM 0.43956 0.943662
302 0T1 0.439024 0.802326
303 COA 0.439024 0.802326
304 12D 0.4375 0.785714
305 FA9 0.4375 0.841463
306 C2R 0.436782 0.90411
307 AMZ 0.436782 0.890411
308 A3S 0.43617 0.810811
309 N6P 0.432692 0.888889
310 PUA 0.430894 0.860759
311 COS 0.428571 0.784091
312 TAP 0.428571 0.883117
313 AMX 0.428571 0.811765
314 1DG 0.428571 0.896104
315 CAO 0.428571 0.775281
316 AIR 0.428571 0.875
317 A6D 0.428571 0.722892
318 DG1 0.428571 0.896104
319 6K6 0.427184 0.90411
320 A3T 0.427083 0.821918
321 NIA 0.426966 0.8
322 649 0.426087 0.744444
323 GTP 0.425743 0.894737
324 SCO 0.425197 0.823529
325 CMX 0.425197 0.823529
326 G2R 0.424528 0.860759
327 GDP 0.424242 0.894737
328 7RA 0.423913 0.930556
329 OXK 0.423077 0.804598
330 0UM 0.423077 0.719512
331 8Q2 0.422414 0.772727
332 FCX 0.421875 0.795455
333 FAM 0.421875 0.784091
334 ACO 0.421875 0.775281
335 GCP 0.421569 0.871795
336 NAP 0.420635 0.918919
337 SXZ 0.420561 0.731707
338 GNH 0.42 0.883117
339 62X 0.419048 0.686047
340 A U 0.418803 0.87013
341 APU 0.418803 0.87013
342 HAX 0.418605 0.784091
343 NVA 2AD 0.418367 0.759494
344 GDC 0.418182 0.884615
345 GKE 0.418182 0.884615
346 GDD 0.418182 0.884615
347 101 0.417582 0.853333
348 GSP 0.417476 0.85
349 3AD 0.416667 0.805556
350 2MC 0.416667 0.75
351 HDV 0.415842 0.868421
352 FYN 0.415385 0.802326
353 3KK 0.415385 0.784091
354 G2Q 0.415094 0.860759
355 K15 0.415094 0.702381
356 NA0 0.414062 0.906667
357 7L1 0.414062 0.775281
358 IVC 0.413534 0.793103
359 S8M 0.413462 0.759494
360 NHD 0.413223 0.905405
361 7RP 0.413043 0.901408
362 MCD 0.412214 0.804598
363 SOP 0.412214 0.784091
364 CA6 0.412214 0.71134
365 COK 0.412214 0.784091
366 1VU 0.409091 0.775281
367 CO6 0.409091 0.784091
368 NMX 0.409091 0.741935
369 CMC 0.409091 0.804598
370 AS 0.408602 0.810127
371 QQY 0.406593 0.815789
372 ACK 0.406593 0.861111
373 6YU 0.40625 0.734043
374 CAJ 0.406015 0.804598
375 SCD 0.406015 0.823529
376 EO7 0.404255 0.788235
377 8BR 0.404255 0.881579
378 GNP 0.403846 0.871795
379 9GM 0.403846 0.871795
380 APX 0.40367 0.907895
381 KB1 0.40367 0.719512
382 TM1 0.40367 0.77381
383 SLU 0.403226 0.770115
384 BCO 0.402985 0.784091
385 MLC 0.402985 0.804598
386 3HC 0.402985 0.793103
387 1HE 0.402985 0.766667
388 A1S 0.402985 0.784091
389 1CZ 0.402878 0.795455
390 CC5 0.402439 0.816901
391 NMN AMP PO4 0.401639 0.87013
392 FAQ 0.40146 0.784091
393 COO 0.4 0.784091
394 YE1 0.4 0.793103
395 MCA 0.4 0.795455
396 CAA 0.4 0.793103
397 2BA 0.4 0.915493
398 CMP 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3IID; Ligand: APR; Similar sites found with APoc: 156
This union binding pocket(no: 1) in the query (biounit: 3iid.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 5YSI NCA None
2 1LSS NAD None
3 2DT9 THR None
4 1P0Z FLC None
5 2IMG MLT None
6 1D1Q 4NP None
7 3K6V CIT 1.4218
8 1HSL HIS 1.4218
9 1UJ5 5RP 1.89573
10 6B5K TYD 1.89573
11 1UTJ ABN 1.89573
12 2G77 AF3 1.89573
13 5HJM MTA 1.89573
14 3CQL NAG 2.36967
15 2J5V PCA 2.36967
16 1H70 CIR 2.36967
17 2VAR KDG 2.36967
18 2YVK MRU 2.36967
19 2VAR KDF 2.36967
20 1PNO NAP 2.77778
21 4BQS K2Q 2.84091
22 3B9Q MLI 2.8436
23 2F5X ASP 2.8436
24 1TE2 PGA 2.8436
25 2D24 XYS XYS 2.8436
26 4O48 ASP 2.8436
27 1PJS NAD 2.8436
28 5Z2L NDP 2.8436
29 4YAG NAI 2.8436
30 5U97 PIT 3.31754
31 2WZM NA7 3.31754
32 1TL2 NDG 3.31754
33 3BY9 SIN 3.31754
34 1BG2 ADP 3.31754
35 3EGI ADP 3.39806
36 5H4S RAM 3.79147
37 4L2H AR6 AR6 3.79147
38 5HRA DAS 3.79147
39 4D52 GIV 3.79147
40 4P6G 2FZ 3.79147
41 1M3U KPL 3.79147
42 1ZGS XMM 3.79147
43 1G55 SAH 3.79147
44 5WP5 SAH 3.79147
45 3AB4 THR 3.93258
46 2DTJ THR 3.93258
47 2KIN ADP 4
48 4WOH 4NP 4.21687
49 5YLF BGC 4.2654
50 1T9D P22 4.2654
51 3H8V ATP 4.2654
52 3DXY SAM 4.2654
53 3IP8 B85 4.2654
54 1YBH P22 4.2654
55 5WKC TP9 4.2654
56 4LRZ ADP 4.2654
57 3LCC SAH 4.2654
58 3PT9 SAH 4.2654
59 1NXJ TLA 4.37158
60 1UYY BGC BGC 4.58015
61 2B4D COA 4.67836
62 1KC7 PPR 4.73934
63 1QAN SAH 4.73934
64 2G36 TRP 4.73934
65 2XZ9 PYR 4.73934
66 3OID NDP 4.73934
67 1VBH PEP 4.73934
68 2JK0 ASP 4.73934
69 1P9B HDA 4.73934
70 2BGM MAX 4.73934
71 1XHL NDP 4.73934
72 1VKF CIT 4.78723
73 3VV5 SLZ 5.21327
74 2Q0L NAP 5.21327
75 2VDV SAM 5.21327
76 5OPM DTP 5.21327
77 1LCF OXL 5.21327
78 3CQ5 PMP 5.21327
79 2YG3 FAD 5.21327
80 1DJL NAP 5.31401
81 1LZR NAG NAG NAG NAG 5.38462
82 1Q9I FAD 5.42907
83 1Q9I TEO 5.42907
84 1TH8 ADP 5.51724
85 2JFN GLU 5.61404
86 3G5N PB2 5.6872
87 5NM7 GLY 5.6872
88 6HH6 A3R 5.6872
89 1D4O NAP 5.97826
90 1V59 NAD 6.16114
91 4RDH AMP 6.16114
92 4D79 ATP 6.16114
93 3KIF GDL 6.60377
94 3A06 FOM 6.63507
95 2GZ3 NAP 6.63507
96 3T7S SAM 6.63507
97 1OJ4 ANP 7.109
98 4YMU ATP 7.109
99 2WW4 ADP 7.109
100 4DPL NAP 7.109
101 3V0H I3P 7.58294
102 3PA8 621 7.58294
103 1ZQ9 SAM 7.58294
104 3MMH SME 7.78443
105 3LN9 FLC 7.91367
106 3L6C MLI 8.05687
107 4RF7 ARG 8.05687
108 1G7C 5GP 8.05687
109 5ZI9 FLC 8.05687
110 3ENV ABF 8.05687
111 2EFJ SAH 8.05687
112 4KRI SAH 8.05687
113 2C3H GLC GLC 8.16327
114 3EWR APR 8.33333
115 1APZ ASP 8.53081
116 1KJ8 GAR 8.53081
117 1D4D FAD 8.53081
118 2GEK GDP 8.53081
119 3FJG 3PG 8.53081
120 4L50 D8X 8.53081
121 1O8B ABF 8.53081
122 2HXW FLC 8.53081
123 3THR C2F 8.53081
124 2OFW ADX 8.65385
125 3K5I AIR 8.68486
126 3SIG AR6 9.00474
127 2X5D PLP 9.47867
128 4BHL ARG 9.47867
129 2H5Z CTO 9.83607
130 5YF1 SFG 9.95261
131 3ITJ CIT 10.4265
132 1LK7 DER 10.4265
133 3EWP APR 10.7345
134 1IXE COA 10.9005
135 2YVJ NAI 11.0092
136 4TQK NAG 11.8483
137 4BGB ADP 12.3223
138 5Z5I XYP 12.3223
139 1NM5 NAD 12.7962
140 2OOR TXP 12.7962
141 1FQK ALF 12.7962
142 5O74 GDP 13.3333
143 1XXA ARG 14.1026
144 3ICS ADP 15.1659
145 3ICT ADP 15.1659
146 5LMK 6ZK 17.0616
147 5ZYN FAD 17.5355
148 3GFS FMN 21.2644
149 2FAV APR 21.6667
150 1RYO OXL 32.7014
151 2Y65 ADP 35
152 4D86 ADP 37.9147
153 4IQY AR6 39.3365
154 2BFR ADP 40.625
155 4J5R A1R 42.4658
156 5CB3 APR 46.9945
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