Receptor
PDB id Resolution Class Description Source Keywords
3H4L 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF N TERMINAL DOMAIN OF A DNA REPAIR PROTE SACCHAROMYCES CEREVISIAE PMS1 ATP BINDING DNA REPAIR DNA DAMAGE NUCLEUS PHOSPHOPDNA BINDING PROTEIN PROTEIN BINDING
Ref.: FUNCTIONAL RESIDUES ON THE SURFACE OF THE N-TERMINA OF YEAST PMS1. DNA REPAIR V. 9 448 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ANP A:397;
B:397;
Valid;
Valid;
none;
none;
submit data
506.196 C10 H17 N6 O12 P3 c1nc(...
MG A:701;
B:702;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3H4L 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF N TERMINAL DOMAIN OF A DNA REPAIR PROTE SACCHAROMYCES CEREVISIAE PMS1 ATP BINDING DNA REPAIR DNA DAMAGE NUCLEUS PHOSPHOPDNA BINDING PROTEIN PROTEIN BINDING
Ref.: FUNCTIONAL RESIDUES ON THE SURFACE OF THE N-TERMINA OF YEAST PMS1. DNA REPAIR V. 9 448 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3H4L - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3H4L - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3H4L - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ANP; Similar ligands found: 358
No: Ligand ECFP6 Tc MDL keys Tc
1 ANP 1 1
2 A2D 0.810811 0.945205
3 B4P 0.802632 0.945205
4 ADP 0.802632 0.972222
5 AP5 0.802632 0.945205
6 BA3 0.789474 0.945205
7 AU1 0.782051 1
8 ATP 0.772152 0.972222
9 AN2 0.769231 0.986111
10 AQP 0.7625 0.972222
11 5FA 0.7625 0.972222
12 M33 0.759494 0.932432
13 MAP 0.752941 0.972973
14 ACP 0.75 0.945946
15 APR 0.740741 0.945205
16 AR6 0.740741 0.945205
17 ACQ 0.73494 0.945946
18 AD9 0.731707 0.945946
19 SAP 0.731707 0.921053
20 AGS 0.731707 0.921053
21 AMP 0.723684 0.944444
22 A 0.723684 0.944444
23 ATF 0.717647 0.933333
24 ADX 0.716049 0.851852
25 CA0 0.716049 0.92
26 50T 0.707317 0.932432
27 PRX 0.698795 0.87013
28 ABM 0.696203 0.893333
29 AMP MG 0.683544 0.868421
30 AP2 0.679012 0.933333
31 A12 0.679012 0.933333
32 APC 0.678571 0.933333
33 TAT 0.674419 0.933333
34 A22 0.674157 0.958904
35 SRA 0.670886 0.894737
36 SRP 0.670455 0.883117
37 5AL 0.666667 0.906667
38 ADQ 0.659341 0.92
39 A1R 0.659341 0.884615
40 ADP MG 0.654762 0.881579
41 3OD 0.648936 0.92
42 BIS 0.648936 0.909091
43 5SV 0.648352 0.82716
44 BEF ADP 0.647059 0.858974
45 ADP BEF 0.647059 0.858974
46 OAD 0.645161 0.92
47 25L 0.642105 0.958904
48 AMO 0.641304 0.907895
49 G5P 0.636364 0.897436
50 DLL 0.634409 0.906667
51 AHX 0.634409 0.897436
52 00A 0.634409 0.860759
53 ANP MG 0.633333 0.921053
54 ADV 0.632184 0.907895
55 ADP PO3 0.632184 0.917808
56 RBY 0.632184 0.907895
57 NB8 0.631579 0.897436
58 25A 0.630435 0.945205
59 8QN 0.630435 0.906667
60 OOB 0.630435 0.906667
61 G3A 0.626263 0.897436
62 ATP MG 0.625 0.881579
63 4AD 0.623656 0.896104
64 PAJ 0.623656 0.8625
65 LAD 0.621053 0.839506
66 1ZZ 0.614583 0.819277
67 TXA 0.614583 0.907895
68 ME8 0.614583 0.819277
69 GTA 0.613861 0.864198
70 3UK 0.610526 0.894737
71 SON 0.604651 0.907895
72 ADP ALF 0.604396 0.848101
73 ALF ADP 0.604396 0.848101
74 WAQ 0.604167 0.860759
75 PR8 0.604167 0.829268
76 4UV 0.6 0.871795
77 GAP 0.6 0.87013
78 FYA 0.597938 0.881579
79 PTJ 0.597938 0.873418
80 ADP VO4 0.597826 0.906667
81 VO4 ADP 0.597826 0.906667
82 UP5 0.596154 0.896104
83 YAP 0.59596 0.871795
84 FA5 0.59596 0.883117
85 PAP 0.595506 0.958333
86 A4P 0.59434 0.823529
87 XAH 0.59 0.841463
88 4UU 0.588235 0.871795
89 AFH 0.588235 0.8625
90 9SN 0.585859 0.85
91 2A5 0.58427 0.894737
92 T5A 0.583333 0.821429
93 NAI 0.580952 0.884615
94 ITT 0.579545 0.917808
95 ATR 0.577778 0.944444
96 OMR 0.575472 0.831325
97 5AS 0.574713 0.781609
98 YLP 0.571429 0.8
99 48N 0.571429 0.873418
100 AP0 0.570093 0.873418
101 4TC 0.570093 0.873418
102 7D3 0.569767 0.881579
103 ADJ 0.568807 0.831325
104 GNP 0.568421 0.922078
105 DAL AMP 0.568421 0.881579
106 NXX 0.566038 0.907895
107 TXD 0.566038 0.884615
108 NAX 0.566038 0.851852
109 4UW 0.566038 0.839506
110 6V0 0.566038 0.873418
111 DND 0.566038 0.907895
112 XYA 0.565789 0.821918
113 ADN 0.565789 0.821918
114 RAB 0.565789 0.821918
115 AOC 0.564706 0.8
116 7D4 0.561798 0.881579
117 ADP BMA 0.561224 0.894737
118 TXE 0.560748 0.884615
119 TYM 0.560748 0.883117
120 YLB 0.555556 0.8
121 YLC 0.555556 0.819277
122 139 0.554545 0.851852
123 5N5 0.551282 0.797297
124 JB6 0.55 0.860759
125 LAQ 0.54717 0.819277
126 MYR AMP 0.544554 0.797619
127 A4D 0.544304 0.797297
128 5CD 0.544304 0.783784
129 7MD 0.542857 0.864198
130 6AD 0.542553 0.886076
131 A2R 0.541667 0.958904
132 UPA 0.541284 0.884615
133 YLA 0.540541 0.8
134 A A 0.54 0.918919
135 COD 0.539823 0.793103
136 BTX 0.539823 0.821429
137 G5A 0.537634 0.781609
138 CNA 0.535714 0.907895
139 AYB 0.535714 0.790698
140 3DH 0.535714 0.753247
141 BT5 0.535088 0.811765
142 ATP A A A 0.533981 0.905405
143 IOT 0.531532 0.811765
144 MTA 0.53012 0.753247
145 3AM 0.529412 0.90411
146 A3P 0.52809 0.944444
147 NAD 0.526316 0.906667
148 PPS 0.526316 0.851852
149 EP4 0.52439 0.734177
150 7D5 0.52381 0.855263
151 AMP DBH 0.52381 0.87013
152 J7C 0.522727 0.75
153 A5A 0.520833 0.809524
154 EAD 0.520661 0.851852
155 TSB 0.520408 0.821429
156 AHZ 0.518519 0.797619
157 M2T 0.518072 0.716049
158 DTA 0.518072 0.766234
159 A3D 0.517241 0.894737
160 6RE 0.517241 0.740741
161 YLY 0.516949 0.790698
162 SSA 0.515464 0.802326
163 NA7 0.514852 0.933333
164 TYR AMP 0.514286 0.858974
165 AR6 AR6 0.514019 0.893333
166 7MC 0.513514 0.843373
167 A2P 0.511111 0.930556
168 52H 0.510204 0.781609
169 VMS 0.510204 0.790698
170 54H 0.510204 0.790698
171 TAD 0.509259 0.8625
172 NAQ 0.508333 0.85
173 A3N 0.505618 0.766234
174 AV2 0.505155 0.893333
175 5CA 0.50505 0.802326
176 53H 0.50505 0.781609
177 ARU 0.504951 0.839506
178 ARG AMP 0.504587 0.809524
179 ZID 0.504132 0.894737
180 P1H 0.504 0.831325
181 3AT 0.5 0.945205
182 NAE 0.5 0.871795
183 AVV 0.5 0.873418
184 P5A 0.495146 0.747253
185 DSZ 0.49505 0.802326
186 LSS 0.49505 0.764045
187 NSS 0.49505 0.802326
188 N0B 0.491803 0.8
189 AF3 ADP 3PG 0.491071 0.817073
190 LA8 ALF 3PG 0.491071 0.817073
191 ALF ADP 3PG 0.491071 0.817073
192 NVA LMS 0.490196 0.764045
193 DAT 0.489362 0.881579
194 IMO 0.488889 0.90411
195 ZAS 0.488636 0.792208
196 FDA 0.488372 0.813953
197 NAJ PZO 0.487395 0.85
198 4TA 0.487179 0.788235
199 LPA AMP 0.486486 0.797619
200 LEU LMS 0.485437 0.764045
201 DTP 0.484536 0.881579
202 V3L 0.484536 0.945205
203 GJV 0.483516 0.731707
204 S4M 0.483516 0.651685
205 DZD 0.483051 0.8625
206 2AM 0.482759 0.917808
207 5AD 0.481013 0.726027
208 KAA 0.480769 0.755556
209 GSU 0.480769 0.781609
210 NDE 0.480315 0.907895
211 M24 0.479339 0.851852
212 MAO 0.478261 0.761905
213 DSH 0.477778 0.707317
214 NEC 0.477778 0.727273
215 FAD 0.477273 0.831325
216 FAS 0.477273 0.831325
217 RGT 0.476636 0.933333
218 0WD 0.474576 0.897436
219 G A A A 0.474576 0.85
220 FNK 0.474074 0.786517
221 5X8 0.473684 0.74359
222 6FA 0.473282 0.821429
223 FB0 0.472868 0.786517
224 NDC 0.472868 0.85
225 YSA 0.472222 0.781609
226 7DD 0.468085 0.958333
227 OVE 0.466667 0.881579
228 NAD IBO 0.466102 0.848101
229 MHZ 0.463158 0.701149
230 A3G 0.461538 0.779221
231 6C6 0.459184 0.858974
232 U A G G 0.458333 0.860759
233 SFG 0.458333 0.730769
234 7D7 0.45679 0.723684
235 128 0.45614 0.8
236 SFD 0.455224 0.736842
237 DDS 0.454545 0.855263
238 GDP 0.454545 0.896104
239 6IA 0.454545 0.817073
240 NJP 0.453782 0.921053
241 ODP 0.453782 0.886076
242 7DT 0.453608 0.958333
243 A7D 0.452632 0.75641
244 Z5A 0.452381 0.802326
245 WSA 0.452174 0.790698
246 7C5 0.45045 0.797468
247 FAY 0.449275 0.841463
248 NDP 0.449153 0.897436
249 A5D 0.44898 0.766234
250 SA8 0.44898 0.690476
251 NAJ PYZ 0.448 0.851852
252 71V 0.446809 0.884615
253 GGZ 0.446602 0.804878
254 RFL 0.446043 0.802326
255 2SA 0.445545 0.907895
256 AMP NAD 0.444444 0.858974
257 GP3 0.444444 0.897436
258 SAI 0.444444 0.716049
259 SAH 0.444444 0.725
260 A A A 0.443396 0.881579
261 PO4 PO4 A A A A PO4 0.443396 0.878378
262 4YB 0.442478 0.764045
263 GTP 0.441176 0.896104
264 SMM 0.441176 0.670455
265 S7M 0.441176 0.674419
266 Y3J 0.440476 0.706667
267 SAM 0.44 0.674419
268 649 0.439655 0.747253
269 12D 0.438596 0.809524
270 A3S 0.4375 0.789474
271 NPW 0.436975 0.864198
272 GCP 0.436893 0.873418
273 AAT 0.435644 0.690476
274 EEM 0.435644 0.674419
275 GNH 0.435644 0.909091
276 DCA 0.435484 0.804598
277 ETB 0.435484 0.813953
278 N6P 0.433962 0.890411
279 TXP 0.433333 0.897436
280 NZQ 0.433333 0.886076
281 PGS 0.43299 0.860759
282 APU 0.432203 0.871795
283 PUA 0.432 0.8625
284 62F 0.431655 0.841463
285 F2N 0.431507 0.795455
286 DA 0.430108 0.855263
287 D5M 0.430108 0.855263
288 J7V 0.429688 0.813953
289 NIA 0.428571 0.848101
290 6K6 0.428571 0.905405
291 A3T 0.428571 0.8
292 0T1 0.428571 0.804598
293 COA 0.428571 0.804598
294 P5F 0.427586 0.804598
295 AAM 0.425532 0.944444
296 0UM 0.424528 0.682353
297 G1R 0.423077 0.884615
298 AMZ 0.422222 0.891892
299 C2R 0.422222 0.88
300 A U 0.420168 0.848101
301 IDP 0.42 0.894737
302 GSP 0.419048 0.851852
303 COS 0.418605 0.786517
304 CAO 0.418605 0.777778
305 AMX 0.418605 0.813953
306 30N 0.418605 0.736842
307 DG1 0.418605 0.897436
308 1DG 0.418605 0.897436
309 TM1 0.418182 0.797619
310 A6D 0.416667 0.746988
311 K15 0.416667 0.666667
312 V1N 0.415929 0.893333
313 SCO 0.415385 0.804598
314 CMX 0.415385 0.804598
315 GEK 0.415094 0.719512
316 NHD 0.414634 0.881579
317 XNP 0.414634 0.851852
318 AIR 0.413793 0.876712
319 COK 0.413534 0.786517
320 G2R 0.412844 0.8625
321 FCX 0.412214 0.777778
322 FAM 0.412214 0.786517
323 ACO 0.412214 0.777778
324 NAP 0.410853 0.92
325 CNV FAD 0.409722 0.775281
326 FA9 0.409396 0.843373
327 SXZ 0.409091 0.694118
328 HAX 0.409091 0.806818
329 PLP AAD 0.408 0.744444
330 TAP 0.407692 0.884615
331 2MC 0.407407 0.752688
332 62X 0.407407 0.651685
333 GKE 0.40708 0.8625
334 GDD 0.40708 0.8625
335 GDC 0.40708 0.8625
336 FYN 0.406015 0.804598
337 3KK 0.406015 0.786517
338 U G A 0.405797 0.819277
339 NA0 0.40458 0.907895
340 101 0.404255 0.855263
341 G 0.40404 0.883117
342 5GP 0.40404 0.883117
343 MGP 0.403846 0.8625
344 MCD 0.402985 0.786517
345 OXK 0.402985 0.786517
346 CA6 0.402985 0.714286
347 SOP 0.402985 0.786517
348 3AD 0.402299 0.783784
349 S8M 0.401869 0.78481
350 YE1 0.40146 0.795455
351 1VU 0.4 0.777778
352 2VA 0.4 0.779221
353 CMC 0.4 0.786517
354 7RP 0.4 0.902778
355 GMV 0.4 0.873418
356 6G0 0.4 0.8625
357 CO6 0.4 0.786517
358 NMX 0.4 0.782609
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3H4L; Ligand: ANP; Similar sites found: 84
This union binding pocket(no: 1) in the query (biounit: 3h4l.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4GCZ ADP 0.000001599 0.56892 1.63488
2 2ZKJ ADP 0.000002881 0.4311 1.63488
3 3QDK QDK 0.01126 0.43046 1.63488
4 2CXG GLC GLC 0.013 0.42061 1.90736
5 5X8G S0N 0.0231 0.40212 1.90736
6 4WGF HX2 0.01209 0.42911 1.95122
7 3B5J 12D 0.01942 0.40958 2.05761
8 1QZR CDX 0.0002549 0.50538 2.17984
9 1QZR ANP 0.00002899 0.50538 2.17984
10 1QY8 RDI 0.00001482 0.48096 2.23048
11 2GFD RDA 0.00001635 0.48958 2.54237
12 4BIX ADP 0.0002518 0.4058 2.68456
13 1JJ7 ADP 0.01299 0.42508 2.69231
14 1P7T PYR 0.01341 0.4191 2.7248
15 1D8C GLV 0.0109 0.40811 2.7248
16 4FXQ G9L 0.03059 0.40077 2.7248
17 2YJP CYS 0.03251 0.40029 3.09278
18 2YPI PGA 0.01365 0.40881 3.23887
19 4IJ6 SEP 0.02165 0.4064 3.31754
20 4BI7 PGA 0.02444 0.40026 3.50195
21 3CBC DBS 0.02869 0.40521 3.53535
22 1Q3Q ANP 0.008476 0.40169 3.54223
23 2D2F ADP 0.006723 0.44516 3.6
24 4IVG ANP 0.000000591 0.54585 4.08719
25 4IPE ANP 0.0000008081 0.5314 4.08719
26 1JQN DCO 0.01445 0.40369 4.08719
27 2DT9 THR 0.008223 0.42406 4.19162
28 1I58 ADP 0.00003316 0.52266 4.2328
29 1I58 ACP 0.000105 0.47346 4.2328
30 1GKZ ADP 0.0000003367 0.59142 4.35967
31 1SW0 PGA 0.01565 0.40203 4.43548
32 4FHT DHB 0.01852 0.41373 4.4586
33 1Q19 SSC 0.009471 0.42811 4.63215
34 2C2A ADP 0.000006703 0.54129 4.65116
35 1Y8O ADP 0.0000001657 0.64835 4.6875
36 2J5V PCA 0.01163 0.43046 4.90463
37 5IDM ANP 0.00000003482 0.5909 5.02793
38 1QDS PGA 0.015 0.4068 5.17928
39 3CM2 X23 0.03106 0.40339 5.38462
40 2AWN ADP 0.01389 0.42221 5.44959
41 5E5U MLI 0.01046 0.42381 5.52764
42 2BTM PGA 0.01822 0.4067 5.55556
43 2OG2 MLI 0.02896 0.4146 5.57103
44 3A4M ADP 0.02205 0.40672 5.76923
45 3AB4 THR 0.01147 0.41682 5.93824
46 4URL XAM 0.00008938 0.44939 5.99455
47 1KIJ NOV 0.0009443 0.43758 5.99455
48 3P7G MAN 0.01 0.42596 6.16438
49 3EHG ATP 0.0004784 0.47418 6.25
50 4NZ6 DGL 0.01522 0.41728 6.38978
51 2HKJ RDC 0.000001292 0.49515 6.53951
52 4ZVI 4S4 0.0001825 0.47266 6.53951
53 2ILZ GTP 0.01641 0.40899 6.53951
54 1S16 ANP 0.00001007 0.49879 7.08447
55 1ZXM ANP 0.00002466 0.46185 7.62943
56 1GXU 2HP 0.01005 0.40437 7.69231
57 2IOR ADP 0.000002005 0.61421 8.08511
58 3CV2 OXL 0.006268 0.43974 8.99183
59 2XCM ADP 0.000001678 0.58282 9.45946
60 3NOJ PYR 0.0165 0.4214 9.66387
61 3A0T ADP 0.00001321 0.49883 9.86842
62 4URN NOV 0.00007075 0.53485 10.2222
63 4WZ6 ATP 0.02917 0.40308 10.3448
64 3D36 ADP 0.00001399 0.52111 11.0656
65 1BGQ RDC 0.00006422 0.44727 11.1111
66 4BAE RWX 0.0001081 0.43217 11.2195
67 4EMV 0R9 0.0006164 0.4497 11.5044
68 1EXF GLY 0.009825 0.40707 11.5702
69 1KZN CBN 0.0001412 0.45788 11.7073
70 4HY1 19X 0.00006583 0.51512 11.7166
71 4B6C B5U 0.0001457 0.47692 11.7347
72 1G6H ADP 0.009539 0.43181 12.4514
73 4PL9 ADP 0.00009102 0.44514 13.1148
74 3TTZ 07N 0.0005932 0.41025 13.1313
75 4P8O 883 0.0001945 0.41491 13.369
76 1S14 NOV 0.00009691 0.52784 13.4021
77 4GGL CJC 0.0003161 0.47721 13.4884
78 1YC4 43P 0.000001813 0.58926 14.0152
79 1ID0 ANP 0.00004134 0.52472 14.4737
80 3NMQ 7PP 0.0001059 0.49926 15.8996
81 4B7P 9UN 0.000009141 0.5557 16.087
82 1TID ATP 0.000002811 0.55804 21.8487
83 1TH8 ADP 0.000000931 0.61185 23.2759
84 1B63 ANP 0.00000001158 0.62405 47.7477
Pocket No.: 2; Query (leader) PDB : 3H4L; Ligand: ANP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3h4l.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3H4L; Ligand: ANP; Similar sites found: 6
This union binding pocket(no: 3) in the query (biounit: 3h4l.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2W92 NGT 0.03126 0.40502 2.17984
2 2CWH NDP 0.009653 0.40815 2.33236
3 2CWH PYC 0.01437 0.40513 2.33236
4 5G5G FAD 0.02516 0.4017 3.93013
5 3KXW 1ZZ 0.01126 0.40244 4.08719
6 1N8V BDD 0.006589 0.41632 8.03571
Pocket No.: 4; Query (leader) PDB : 3H4L; Ligand: ANP; Similar sites found: 15
This union binding pocket(no: 4) in the query (biounit: 3h4l.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B2D SER 0.01775 0.40197 1.90736
2 1YOK P6L 0.03242 0.40655 1.95312
3 1S20 TLA 0.01667 0.40716 2.05882
4 5LLT DND 0.01613 0.41781 2.34742
5 4XJ7 ADN 0.008251 0.40753 4.11985
6 5CFQ 1SY 0.03334 0.40278 4.27807
7 1FCH TYR GLN SER LYS LEU 0.01027 0.42115 4.35967
8 3EHH ADP 0.000538 0.45433 5.04587
9 2ZFZ ARG 0.03441 0.43945 5.06329
10 1M3U KPL 0.007404 0.41185 5.30303
11 4X1T UDP 0.01107 0.40583 6.12745
12 4X6F 3XU 0.04708 0.4009 6.66667
13 2GBB CIT 0.01109 0.40341 7.05128
14 5A5W GUO 0.0237 0.41753 9.88142
15 4HZ0 1AV 0.0001671 0.43243 12.2066
Feedback