Receptor
PDB id Resolution Class Description Source Keywords
2IDO 2.1 Å EC: 2.7.7.7 STRUCTURE OF THE E. COLI POL III EPSILON-HOT PROOFREADING CO ESCHERICHIA COLI POLYMERASE EXONUCLEASE HOT EPSILON POL III TRANSFERASE
Ref.: STRUCTURE OF THE ESCHERICHIA COLI DNA POLYMERASE II EPSILON-HOT PROOFREADING COMPLEX. J.BIOL.CHEM. V. 281 38466 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO C:1000;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN A:1001;
A:1002;
C:1003;
C:1004;
C:1005;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
TMP A:2001;
C:2002;
Valid;
Valid;
none;
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
2IDO 2.1 Å EC: 2.7.7.7 STRUCTURE OF THE E. COLI POL III EPSILON-HOT PROOFREADING CO ESCHERICHIA COLI POLYMERASE EXONUCLEASE HOT EPSILON POL III TRANSFERASE
Ref.: STRUCTURE OF THE ESCHERICHIA COLI DNA POLYMERASE II EPSILON-HOT PROOFREADING COMPLEX. J.BIOL.CHEM. V. 281 38466 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 2IDO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 2IDO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 2IDO - TMP C10 H15 N2 O8 P CC1=CN(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 : 2IDO; Ligand: TMP; Similar sites found: 81
This union binding pocket(no: 1) in the query (biounit: 2ido.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1T57 FMN 0.02693 0.40701 2.15054
2 1UNH IXM 0.01834 0.40388 2.68817
3 1SR7 MOF 0.04709 0.40218 2.68817
4 5F5N NAD 0.02634 0.41305 3.61446
5 1EBG PAH 0.02303 0.40249 3.61446
6 1P9P SAH 0.01244 0.41963 3.76344
7 3TKI S25 0.04704 0.41654 3.76344
8 2RDG NDG FUC SIA GAL 0.007381 0.4095 3.76344
9 2J8C SPO 0.04105 0.42946 4.81928
10 4ZGS NAD 0.03644 0.40107 5.37634
11 1KQR MNA 0.01645 0.40161 5.58659
12 5APK 76E 0.02211 0.4174 5.91398
13 5APJ 76E 0.02194 0.41705 5.91398
14 5NTW 98N 0.03112 0.41152 5.91398
15 3SVJ 4LI 0.0196 0.40975 5.91398
16 4ZOM 4Q3 0.03382 0.40466 5.91398
17 2HBL AMP 0.0001352 0.5074 6.0241
18 5U6C 7YS 0.0249 0.40589 6.0241
19 2ZKJ ADP 0.03596 0.41372 6.45161
20 2RDE C2E 0.01194 0.41321 6.45161
21 3JRS A8S 0.004975 0.44052 6.98925
22 2FZH DH1 0.02115 0.4323 6.98925
23 5FBN 5WF 0.02905 0.4137 6.98925
24 4NS3 NAD 0.02209 0.40557 6.98925
25 2C43 COA 0.0391 0.40103 7.22892
26 2Q7D ANP 0.03824 0.40012 7.22892
27 2CWH NDP 0.01786 0.42357 7.52688
28 2GOU FMN 0.04555 0.40453 7.52688
29 4OKE AMP 0.0002313 0.41336 7.7381
30 3NW7 LGV 0.04506 0.41154 8.43373
31 3WCA FPS 0.01105 0.43728 8.60215
32 5VC5 96M 0.01073 0.4331 9.13978
33 2GBB CIT 0.01194 0.40912 9.61539
34 1ZCB GDP 0.004634 0.4487 9.63855
35 4M0R 644 0.01913 0.4353 9.63855
36 4B7P 9UN 0.03521 0.42257 9.63855
37 4OIC A8S 0.0163 0.41157 9.63855
38 4YZC STU 0.03642 0.41144 9.63855
39 3DEK RXD 0.02631 0.41032 9.63855
40 5UR1 YY9 0.03302 0.40665 9.63855
41 4P6X HCY 0.0186 0.41398 10.2151
42 1JR8 FAD 0.02252 0.41218 10.2564
43 1OUW MLT 0.004337 0.41911 10.5263
44 1SVK ALF GDP 0.02751 0.40777 10.8434
45 4AUA 4AU 0.01959 0.40408 10.8434
46 4UP3 FAD 0.03491 0.41614 11.2903
47 1N20 3AG 0.008338 0.43367 11.828
48 5MW4 5JU 0.02101 0.43472 12.0482
49 3NMV PYV 0.02091 0.40568 12.0482
50 1CMC SAM 0.04011 0.40272 12.5
51 3D78 NBB 0.01195 0.44029 12.605
52 1U70 NDP 0.01509 0.44124 13.253
53 1KBJ FMN 0.01674 0.42158 13.253
54 1KBI PYR 0.02141 0.41787 13.253
55 5HCY 60D 0.04117 0.41176 13.253
56 4ZEV M6P 0.01131 0.41506 13.9785
57 2W9S NDP 0.03475 0.40344 14.2857
58 1KQ4 FAD 0.005616 0.44277 14.4578
59 2WJH FLC 0.01892 0.40329 14.4578
60 5N87 N66 0.04119 0.40915 14.5161
61 5JO1 6LM 0.01269 0.42399 15.6627
62 3RI1 3RH 0.02588 0.41187 15.6627
63 4CZG QH3 0.03213 0.41077 16.6667
64 4CZG ADP 0.03085 0.41077 16.6667
65 1ZC3 GNP 0.0332 0.40438 17.6991
66 1KOJ PAN 0.02132 0.40602 18.0723
67 5M45 AMP 0.0258 0.40054 18.0723
68 4HDQ GNP 0.02544 0.4125 19.2308
69 2XOD FMN 0.02369 0.40498 19.2771
70 4O1M NAD 0.04503 0.40269 19.3548
71 1W0H AMP 0.00006935 0.52566 20.4301
72 5KMS FAD 0.04924 0.40645 21.5054
73 3PTG 932 0.009595 0.41179 21.6867
74 3AMN CBK 0.03185 0.40055 27.7108
75 3AMN CBI 0.03185 0.40055 27.7108
76 4BHN BH9 0.01072 0.42311 28.9157
77 5UOX 8GY 0.01903 0.41211 28.9157
78 3B6O TMP 0.000000006051 0.65587 29.0323
79 4FF8 14S 0.01259 0.41173 30.1205
80 1WLJ U5P 0.000497 0.44972 31.1828
81 4J7Q B7N 0.0164 0.43306 39.759
Pocket No.: 2; Query (leader) PDB : 2IDO; Ligand: TMP; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 2ido.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N8V KZZ 0.009894 0.40997 None
2 5JNN 6LM 0.02924 0.40473 1.6129
3 3G9E RO7 0.02681 0.41916 2.68817
4 5CHR 4NC 0.01225 0.40796 2.91971
5 4RHP PEF 0.01832 0.40599 3.76344
6 4USF 6UI 0.02962 0.40468 4.81928
7 4IGH 1EA 0.04404 0.42747 4.83871
8 4IGH ORO 0.04404 0.42747 4.83871
9 4IGH FMN 0.04404 0.42747 4.83871
10 4DXG NDG FUC SIA GAL 0.01192 0.40336 4.83871
11 3EBL GA4 0.02974 0.40094 7.22892
12 3W68 VIV 0.02422 0.4053 7.52688
13 1TB3 FMN 0.02593 0.41534 8.43373
14 3WUR O4B 0.008 0.41001 8.43373
15 4KCF AKM 0.03349 0.40315 8.43373
16 4QWT ACD 0.03737 0.40282 8.43373
17 5C2H 4XU 0.04633 0.4044 9.13978
18 1OBD AMP 0.01706 0.40086 9.13978
19 1YOK P6L 0.02163 0.42551 9.63855
20 5UNJ RJW 0.01327 0.41289 9.63855
21 4XSH NAI 0.02186 0.41111 9.63855
22 5G3N X28 0.02991 0.40209 10.2362
23 1PNO NAP 0.04833 0.40287 10.8434
24 4DV8 0LX 0.04344 0.40615 12.0482
25 4WZH FMN 0.03472 0.40397 12.0482
26 4MCC 21X 0.02422 0.41334 12.3656
27 4X7G 3Y8 0.04216 0.40829 14.4578
28 3G5D 1N1 0.01733 0.44337 16.8675
29 3BIY 01K 0.03176 0.40187 17.2043
30 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.0354 0.4063 18.0723
31 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.04335 0.40476 18.0723
32 1YKD CMP 0.01579 0.41135 19.2771
33 3BEJ MUF 0.02173 0.41106 20
34 5X2Z 3LM 0.03996 0.40077 22.8916
35 4OKZ 3E9 0.01127 0.42612 25.3012
36 5IR4 ZPE 0.03864 0.41728 26.506
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