Receptor
PDB id Resolution Class Description Source Keywords
2QXF 1.5 Å EC: 3.1.11.1 PRODUCT BOUND STRUCTURE OF EXONUCLEASE I AT 1.5 ANGSTROM RES ESCHERICHIA COLI ALPHA-BETA DOMAIN DNAQ SUPERFAMILY SH3-LIKE DOMAIN PRODUCSTRUCTURE DNA DAMAGE DNA REPAIR EXONUCLEASE HYDROLASE
Ref.: STRUCTURE OF ESCHERICHIA COLI EXONUCLEASE I IN COMP THYMIDINE 5'-MONOPHOSPHATE. ACTA CRYSTALLOGR.,SECT.D V. 64 206 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:2000;
A:2001;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NA A:2002;
Part of Protein;
none;
submit data
22.99 Na [Na+]
TMP A:3000;
Valid;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HP9 1.6 Å EC: 3.1.11.1 CRYSTAL STRUCTURE OF SSB/EXONUCLEASE I IN COMPLEX WITH INHIB ESCHERICHIA COLI EXONUCLEASE SSB GENOME MAINTENANCE DNA DAMAGE DNA REPAIRHYDROLASE NUCLEASE
Ref.: SMALL-MOLECULE TOOLS FOR DISSECTING THE ROLES OF SS INTERACTIONS IN GENOME MAINTENANCE PROC.NATL.ACAD.SCI.USA V. 107 633 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3HL8 Ki = 32 uM BBP C14 H16 Cl N3 O S CC(C)(C)C1....
2 2QXF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 3HP9 Ki = 26 uM CF1 C15 H11 Cl F3 N O3 COc1ccc(c(....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3HL8 Ki = 32 uM BBP C14 H16 Cl N3 O S CC(C)(C)C1....
2 2QXF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 3HP9 Ki = 26 uM CF1 C15 H11 Cl F3 N O3 COc1ccc(c(....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3HL8 Ki = 32 uM BBP C14 H16 Cl N3 O S CC(C)(C)C1....
2 2QXF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
3 3HP9 Ki = 26 uM CF1 C15 H11 Cl F3 N O3 COc1ccc(c(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TMP; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 TMP 1 1
2 TYD 0.80597 0.985714
3 TTP 0.760563 0.985714
4 UFP 0.716418 0.917808
5 TBD 0.708333 0.945205
6 5HU 0.705882 0.957747
7 BRU 0.705882 0.917808
8 5IU 0.695652 0.917808
9 THM 0.693548 0.859155
10 LLT 0.693548 0.859155
11 NYM 0.671429 0.971831
12 FDM 0.671429 0.931507
13 THP 0.661972 0.985507
14 TLO 0.654321 0.931507
15 0DN 0.646154 0.84507
16 ATM 0.64 0.906667
17 BVP 0.64 0.957747
18 DAU 0.635294 0.918919
19 18T 0.623529 0.918919
20 1JB 0.623529 0.918919
21 TRH 0.623529 0.918919
22 3R2 0.623529 0.906667
23 TDX 0.623529 0.931507
24 DWN 0.609195 0.894737
25 T3Q 0.609195 0.894737
26 3YN 0.609195 0.918919
27 T3F 0.609195 0.894737
28 T46 0.602273 0.918919
29 0N2 0.602273 0.883117
30 T3P 0.6 0.957143
31 DT DT DT DT DT 0.597701 0.958333
32 MMF 0.595506 0.894737
33 0FX 0.595506 0.894737
34 AKM 0.593407 0.873418
35 UMP 0.583333 0.956522
36 DU 0.583333 0.956522
37 QDM 0.582418 0.883117
38 DT DT PST 0.577778 0.893333
39 FNF 0.576087 0.906667
40 JHZ 0.576087 0.871795
41 1YF 0.576087 0.906667
42 TXS 0.575342 0.8
43 4TG 0.569892 0.906667
44 T3S 0.56 0.8
45 2DT 0.555556 0.971429
46 ATY 0.548781 0.931507
47 DDN 0.547945 0.956522
48 AZD 0.535714 0.894737
49 FUH 0.53 0.894737
50 QUH 0.53 0.894737
51 T5A 0.524272 0.829268
52 DT DT DT 0.52381 0.890411
53 DT ME6 DT 0.509804 0.881579
54 DCM 0.506494 0.890411
55 DC 0.506494 0.890411
56 AZZ 0.5 0.789474
57 4TA 0.495327 0.817073
58 ABT 0.483516 0.871795
59 QBT 0.480519 0.915493
60 WMJ 0.477778 0.75
61 7SG 0.474138 0.851852
62 TQP 0.474138 0.851852
63 T4K 0.470085 0.841463
64 T5K 0.470085 0.841463
65 DUD 0.469136 0.942857
66 UMC 0.467532 0.901408
67 D3T 0.464286 0.957747
68 TPE 0.463158 0.881579
69 D4M 0.461538 0.927536
70 ID2 0.452055 0.786667
71 UC5 0.451219 0.929577
72 DUT 0.447059 0.942857
73 DUP 0.44186 0.916667
74 DUN 0.440476 0.916667
75 ADS THS THS THS 0.433628 0.776471
76 DT MA7 DT 0.42623 0.807229
77 8OG 0.425287 0.82716
78 BVD 0.423077 0.821918
79 74X 0.42 0.72093
80 74W 0.42 0.72093
81 5FU 0.4125 0.84
82 D4D 0.411765 0.914286
83 PAX 0.408333 0.839506
84 YYY 0.406977 0.878378
85 DA DT DA DA 0.404959 0.82716
86 BTD 0.404762 0.759494
87 DPB 0.404494 0.890411
88 DUT MG 0.404494 0.876712
89 5BU 0.402439 0.84
90 3DT 0.4 0.821918
91 DUS 0.4 0.820513
92 UMP AF3 PO4 0.4 0.842105
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HP9; Ligand: CF1; Similar sites found: 212
This union binding pocket(no: 1) in the query (biounit: 3hp9.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.002507 0.44651 None
2 5MT9 SRO 0.03205 0.40725 None
3 5G3N X28 0.0266 0.40699 None
4 1UO4 PIH 0.0014 0.40111 None
5 2FP2 TSA 0.01294 0.41564 1.20482
6 3R9C ECL 0.02874 0.40006 1.43541
7 5IR4 ZPE 0.0118 0.44066 1.45228
8 2OBD 2OB 0.005513 0.47154 1.47059
9 2OBD PCW 0.04644 0.40656 1.47059
10 5D59 78M 0.04392 0.42139 1.65975
11 5X93 K87 0.04093 0.40274 1.72414
12 2ZFU SAH 0.0317 0.40166 1.86047
13 2J62 GSZ 0.01482 0.41975 1.86722
14 2RH1 CLR 0.02697 0.41557 1.86722
15 2WYA HMG 0.0266 0.41829 1.95652
16 3SVJ 4LI 0.01103 0.42938 1.97044
17 1GNI OLA 0.04341 0.46396 2.07469
18 4NKW PLO 0.02025 0.40574 2.07469
19 5JNN 6LM 0.02376 0.41263 2.10526
20 3G4G D71 0.01365 0.42422 2.13777
21 1FCH TYR GLN SER LYS LEU 0.01448 0.43016 2.17391
22 4BVM VCA 0.03272 0.40494 2.25564
23 5V13 JH3 0.0164 0.41231 2.28216
24 2JC9 ADN 0.015 0.40656 2.28216
25 2J4D FAD 0.04445 0.40015 2.28216
26 2NNQ T4B 0.01887 0.44007 2.29008
27 4XVX P33 FDA 0.04423 0.40739 2.31362
28 1N6B DMZ 0.02351 0.40074 2.32558
29 3AHQ FAD 0.00174 0.46801 2.36559
30 5ENQ 5QE 0.01582 0.41878 2.36686
31 1SO2 666 0.01869 0.40925 2.38095
32 5F8F SFG 0.01007 0.42029 2.38727
33 3ET3 ET1 0.01789 0.41507 2.39726
34 2VDY HCY 0.002601 0.41131 2.41287
35 3B1F NAD 0.02431 0.43261 2.41379
36 3CV9 VDX 0.01766 0.42166 2.42718
37 3B1M KRC 0.004625 0.44602 2.4735
38 2VAT COA 0.01569 0.42385 2.47748
39 4HEE 14R 0.007181 0.43925 2.48227
40 4IS0 1R4 0.01158 0.43065 2.48963
41 1N20 3AG 0.01259 0.42404 2.48963
42 4COL DTP 0.01008 0.42313 2.48963
43 3FWN 6PG 0.02031 0.40855 2.5
44 3FUR Z12 0.02892 0.42613 2.57353
45 5TWO 7MV 0.01576 0.41849 2.57353
46 2PRG BRL 0.01269 0.4183 2.58303
47 5K52 OCD 0.01916 0.40987 2.64151
48 5UV1 0FV 0.0162 0.40107 2.6971
49 3TYZ PAB 0.0292 0.40625 2.85714
50 3TYZ XHP 0.02608 0.40625 2.85714
51 4DOO DAO 0.02617 0.40424 2.92683
52 4RW3 PLM 0.0008066 0.47538 2.98013
53 3DLS ADP 0.0135 0.41119 2.98507
54 1N4H REA 0.01988 0.41384 3.0888
55 4QOM PYG 0.006941 0.43776 3.11203
56 3QCJ NX4 0.02524 0.41829 3.22581
57 3ZUY TCH 0.007871 0.42454 3.40557
58 5B0W 22B 0.0009794 0.49356 3.43643
59 5DX3 EST 0.00348 0.44536 3.44828
60 5DKK FMN 0.005933 0.44222 3.44828
61 5DXE EST 0.005776 0.43368 3.44828
62 5DXG EST 0.005339 0.43321 3.44828
63 1M13 HYF 0.0413 0.40971 3.48101
64 5HYR EST 0.004153 0.44265 3.48837
65 4B5P ACO 0.01431 0.43176 3.5
66 4MG7 27H 0.002428 0.46323 3.52941
67 4MG9 27K 0.002086 0.44932 3.52941
68 4MGA 27L 0.001685 0.4432 3.52941
69 4MGB XDH 0.009908 0.42948 3.52941
70 4TUZ 36J 0.03294 0.4011 3.52941
71 3RGA ILD 0.01375 0.43241 3.53357
72 2WPX ACO 0.01655 0.41202 3.53982
73 5AAV GW5 0.0191 0.4377 3.57143
74 2BJ4 OHT 0.007791 0.43545 3.57143
75 4TV1 36M 0.002812 0.44091 3.58566
76 3UUD EST 0.005085 0.43738 3.58566
77 3KDU NKS 0.01277 0.44586 3.61011
78 4AZP A9M 0.01822 0.42203 3.62319
79 2QE4 JJ3 0.01348 0.45431 3.62903
80 5DCH 1YO 0.004087 0.40401 3.64583
81 3QQA TCH 0.03975 0.42431 3.7037
82 3UST FAD 0.00133 0.46133 3.74532
83 3FEI CTM 0.02229 0.41139 3.74532
84 1E4I NFG 0.0004243 0.45975 3.80313
85 1TV5 N8E 0.005995 0.42026 3.83747
86 1BUC CAA 0.01847 0.41876 3.91645
87 2Q8H TF4 0.004365 0.43547 3.94191
88 3KP6 SAL 0.009517 0.41319 3.97351
89 5AZC PGT 0.0238 0.45307 4
90 4DVE BTN 0.008273 0.41485 4.0404
91 4WUJ FMN 0.006545 0.43814 4.08163
92 5UNJ RJW 0.01669 0.41357 4.08163
93 2LBD REA 0.01338 0.42581 4.11985
94 4DL8 UMP AF3 PO4 0.01631 0.41738 4.13793
95 1ZDT PEF 0.03865 0.40881 4.14938
96 1DEK DGP 0.01995 0.40721 4.14938
97 4YZN 4K5 0.02778 0.40475 4.18118
98 5GUE GGS 0.01335 0.42488 4.22961
99 2J8C SPO 0.04161 0.43713 4.23077
100 5X8Q 82R 0.03661 0.40089 4.26357
101 4EKQ NPO 0.01318 0.42051 4.27807
102 5NTW 98N 0.04403 0.40244 4.28016
103 5LGA 6VH 0.01929 0.42836 4.33333
104 5E7V M7E 0.04216 0.40795 4.33333
105 1VG0 GER 0.008457 0.42134 4.34783
106 1JGS SAL 0.01807 0.40663 4.34783
107 4ASE AV9 0.04924 0.40383 4.53258
108 3OV6 MK0 0.02059 0.42433 4.78589
109 5CYV WCA 0.03014 0.40478 4.79452
110 3TD3 GLY 0.0197 0.401 4.87805
111 3V49 PK0 0.02486 0.41562 4.88722
112 4ZOM 4Q3 0.006592 0.45509 4.88889
113 4ZBR NPS 0.01977 0.42925 4.97925
114 1PS9 FMN 0.02648 0.40613 4.97925
115 5VRH OLB 0.004274 0.42594 4.98084
116 2F59 INI 0.02947 0.4054 5.09554
117 4F4S EFO 0.0006843 0.42526 5.26316
118 5K13 6Q7 0.00635 0.44288 5.28455
119 1NF8 BOG 0.00375 0.42946 5.31401
120 1M2Z BOG 0.01941 0.40386 5.44747
121 4P6X HCY 0.02673 0.4048 5.4902
122 3BQD DAY 0.03447 0.4041 5.4902
123 5DJT FMN 0.006788 0.43769 5.51724
124 3CGD COA 0.01739 0.46281 5.625
125 3CGD FAD 0.01739 0.46281 5.625
126 5B4B LP5 0.004588 0.4669 5.64516
127 3FS1 MYR 0.01868 0.40683 5.65217
128 4BKJ STI 0.01008 0.43076 5.71429
129 4RC8 STE 0.01166 0.4336 5.85586
130 2VWA PTY 0.01165 0.40229 5.94059
131 5OCA 9QZ 0.003887 0.43958 6.0166
132 4WN5 MVC 0.01295 0.42505 6.08696
133 3KAP FMN 0.01729 0.41494 6.12245
134 2V95 HCY 0.004503 0.42617 6.19946
135 4ZW9 BGC 0.02346 0.40932 6.22407
136 4ZW9 GLC 0.02346 0.40932 6.22407
137 5IF4 6AK 0.02637 0.41191 6.28931
138 1X0P FAD 0.01674 0.40597 6.29371
139 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.004413 0.43454 6.55738
140 5L7G 6QE 0.01291 0.42645 6.55738
141 4OKZ 3E9 0.03052 0.40147 6.57534
142 4LSJ LSJ 0.02849 0.40896 6.58915
143 4HBM 0Y7 0.02382 0.40293 6.66667
144 5LWY OLB 0.00499 0.43905 6.72269
145 1FM9 570 0.0147 0.43387 6.72269
146 1FM9 9CR 0.009156 0.4311 6.72269
147 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.04434 0.41161 6.73759
148 2Q1H AS4 0.009207 0.434 6.8
149 4RHP PEF 0.02836 0.40126 6.80851
150 4POJ 2VP 0.008425 0.43973 6.92641
151 4M8E 29V 0.009724 0.4338 6.92641
152 3KO0 TFP 0.01042 0.40524 6.93069
153 3H0A 9RA 0.02402 0.4023 7.01754
154 1N8V BDD 0.02421 0.42565 7.14286
155 4UAL 3FV 0.02412 0.40083 7.1599
156 5F1R 42O 0.01782 0.42025 7.173
157 1DB1 VDX 0.03316 0.41457 7.33591
158 4MSG 2C6 0.04905 0.40357 7.37327
159 2I0G I0G 0.01605 0.45237 7.393
160 2E2R 2OH 0.007996 0.45725 7.46888
161 5UN9 NHT 0.01333 0.40469 7.46888
162 5GIC DLC 0.04835 0.40565 7.6
163 1U3R 338 0.01196 0.4237 7.88382
164 2BIF BOG 0.02022 0.41835 7.88913
165 2YJD YJD 0.003817 0.44702 7.91667
166 4J24 EST 0.004826 0.43627 7.91667
167 3OLL EST 0.007051 0.43118 7.91667
168 5LJI FMN 0.02196 0.40324 8.10811
169 3P0K FAD 0.007579 0.43271 8.27068
170 2EW5 Y12 0.02472 0.40431 8.28729
171 1WUB OTP 0.03452 0.41982 8.42697
172 1JR8 FAD 0.002333 0.46828 8.54701
173 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.008371 0.43568 8.55263
174 1OQC FAD 0.005744 0.44793 8.8
175 3RV5 DXC 0.007236 0.41297 8.98876
176 4PYW ACE THR THR ALA ILE NH2 0.02122 0.41473 9.15842
177 5L2J 6UL 0.01583 0.45313 9.18367
178 5L2J 70E 0.01657 0.45313 9.18367
179 3Q8G PEE 0.01942 0.44355 9.375
180 1RV1 IMZ 0.01379 0.41278 9.41177
181 3HY9 098 0.01847 0.4123 9.50226
182 4H07 IPH 0.02809 0.41781 9.74026
183 3WCA FPS 0.00723 0.44554 9.86301
184 3CEV ARG 0.01749 0.40571 10.0334
185 4HIA FMN 0.0295 0.42031 10.2273
186 1C9K 5GP 0.003193 0.43467 10.5556
187 2PZ8 APC 0.02155 0.40478 10.5634
188 1AG9 FMN 0.0183 0.41216 10.8571
189 2BTO GTP 0.01016 0.4353 11.1111
190 3RYC GDP 0.0264 0.40039 11.1888
191 3PVT 3HC 0.01712 0.45865 11.254
192 1SR7 MOF 0.01257 0.44001 11.583
193 2VAR AMP 0.01286 0.41096 11.8211
194 2VAR ANP 0.02277 0.41096 11.8211
195 1ELR ACE MET GLU GLU VAL ASP 0.00838 0.43046 12.2137
196 1CZR FMN 0.01946 0.41034 12.426
197 5ECP ATP 0.008543 0.45206 12.5561
198 3MBG FAD 0.003675 0.46256 12.9496
199 2ALG DAO 0.0009503 0.48734 13.0435
200 2ALG HP6 0.04479 0.40786 13.0435
201 3G08 FEE 0.008005 0.46818 13.1313
202 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 0.002417 0.4878 13.6364
203 5CSD ACD 0.0102 0.4423 13.8365
204 3U5S FAD 0.003501 0.45762 14.2857
205 3O55 FAD 0.004904 0.45349 14.4
206 1L1Q 9DA 0.03288 0.42282 14.5161
207 2D5Z L35 0.02304 0.45569 16.3121
208 5MWE TCE 0.009481 0.41762 17.1429
209 4WQ2 3SU 0.01174 0.41883 17.341
210 5SVV FMN 0.008928 0.4332 24.0876
211 2DYR PGV 0.0237 0.42838 36.1702
212 2DYR PSC 0.02477 0.41455 36.1702
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