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Receptor
PDB id Resolution Class Description Source Keywords
1H5T 1.9 Å EC: 2.7.7.24 THYMIDYLYLTRANSFERASE COMPLEXED WITH THYMIDYLYLDIPHOSPHATE-G ESCHERICHIA COLI TRANSFERASE PYROPHOSPHATASE NUCLEOTIDE SUGAR METHABOLISM
Ref.: KINETIC AND CRYSTALLOGRAPHIC ANALYSES SUPPORT A SEQUENTIAL-ORDERED BI BI CATALYTIC MECHANISM FOR ES COLI GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE J.MOL.BIOL. V. 313 831 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAU A:1293;
B:1293;
C:1293;
D:1293;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
564.329 C16 H26 N2 O16 P2 CC1=C...
SO4 D:1294;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
TYD A:1292;
B:1292;
C:1292;
D:1292;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1H5T 1.9 Å EC: 2.7.7.24 THYMIDYLYLTRANSFERASE COMPLEXED WITH THYMIDYLYLDIPHOSPHATE-G ESCHERICHIA COLI TRANSFERASE PYROPHOSPHATASE NUCLEOTIDE SUGAR METHABOLISM
Ref.: KINETIC AND CRYSTALLOGRAPHIC ANALYSES SUPPORT A SEQUENTIAL-ORDERED BI BI CATALYTIC MECHANISM FOR ES COLI GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE J.MOL.BIOL. V. 313 831 2001
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1H5T - TYD C10 H16 N2 O11 P2 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 4 families.
1 1H5T - TYD C10 H16 N2 O11 P2 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 4 families.
1 1H5T - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAU; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 DAU 1 1
2 1JB 0.788889 0.972973
3 18T 0.788889 0.972973
4 TRH 0.788889 0.972973
5 TDX 0.731183 0.986301
6 0FX 0.71875 0.947368
7 T3Q 0.715789 0.947368
8 T3F 0.715789 0.947368
9 T46 0.708333 0.972973
10 TTP 0.701149 0.932432
11 MMF 0.701031 0.947368
12 TYD 0.694118 0.932432
13 4TG 0.69 0.96
14 QDM 0.686869 0.910256
15 FNF 0.68 0.96
16 1YF 0.68 0.96
17 3R2 0.659794 0.934211
18 3YN 0.646465 0.946667
19 0N2 0.64 0.935065
20 TMP 0.635294 0.918919
21 JHZ 0.631068 0.898734
22 DWN 0.63 0.922078
23 QUH 0.62963 0.947368
24 FUH 0.62963 0.947368
25 TLO 0.618557 0.933333
26 AKM 0.615385 0.9
27 T5K 0.56 0.86747
28 T4K 0.56 0.86747
29 7SG 0.552 0.855422
30 TQP 0.552 0.855422
31 T5A 0.551724 0.855422
32 TBD 0.536842 0.896104
33 THM 0.52381 0.863014
34 LLT 0.52381 0.863014
35 UPG 0.519608 0.891892
36 GDU 0.519608 0.891892
37 UFM 0.519608 0.891892
38 GUD 0.519608 0.891892
39 2GW 0.518182 0.906667
40 DT DT DT 0.509615 0.906667
41 UFP 0.5 0.846154
42 0DN 0.494253 0.8
43 DT DT PST 0.490909 0.860759
44 AZD 0.490196 0.85
45 1GW 0.487179 0.871795
46 DT DT DT DT DT 0.486239 0.907895
47 C5G 0.485981 0.846154
48 ATY 0.485149 0.907895
49 T3P 0.483516 0.905405
50 5HU 0.478723 0.932432
51 THP 0.46875 0.905405
52 4TA 0.464 0.821429
53 BRU 0.463158 0.846154
54 DUT 0.46 0.891892
55 ATM 0.46 0.8375
56 FDM 0.458333 0.858974
57 NYM 0.458333 0.894737
58 5IU 0.458333 0.846154
59 DUD 0.44898 0.891892
60 GDC 0.448276 0.724138
61 GKE 0.448276 0.724138
62 GDD 0.448276 0.724138
63 TPE 0.446429 0.909091
64 D3T 0.445545 0.906667
65 TXS 0.4375 0.759494
66 BVP 0.431373 0.881579
67 T3S 0.428571 0.782051
68 ADQ 0.428571 0.746988
69 DT ME6 DT 0.427419 0.860759
70 ABT 0.423423 0.829268
71 USQ 0.415929 0.785714
72 AZZ 0.412371 0.772152
73 UFG 0.410714 0.846154
74 U2F 0.410714 0.846154
75 UPF 0.410714 0.846154
76 2DT 0.40625 0.893333
77 ADS THS THS THS 0.406015 0.772727
78 UD1 0.403361 0.905405
79 UD2 0.403361 0.905405
Ligand no: 2; Ligand: TYD; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 DAU 0.694118 0.932432
6 1JB 0.682353 0.932432
7 TRH 0.682353 0.932432
8 3R2 0.682353 0.92
9 18T 0.682353 0.932432
10 TDX 0.682353 0.945205
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3Q 0.666667 0.907895
15 T3F 0.666667 0.907895
16 TBD 0.662338 0.958904
17 T46 0.659091 0.932432
18 0N2 0.659091 0.896104
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 THM 0.641791 0.873239
23 LLT 0.641791 0.873239
24 QDM 0.637363 0.896104
25 JHZ 0.630435 0.884615
26 1YF 0.630435 0.92
27 AKM 0.630435 0.886076
28 FNF 0.630435 0.92
29 4TG 0.623656 0.92
30 DT DT DT 0.616279 0.917808
31 DUD 0.61039 0.957143
32 UFP 0.6 0.905405
33 0DN 0.6 0.833333
34 DT DT DT DT DT 0.582418 0.945205
35 QUH 0.58 0.907895
36 FUH 0.58 0.907895
37 T5A 0.572816 0.841463
38 BRU 0.571429 0.905405
39 5HU 0.571429 0.971831
40 DT DT PST 0.569892 0.87013
41 FDM 0.564103 0.918919
42 5IU 0.564103 0.905405
43 NYM 0.564103 0.958333
44 T3P 0.56 0.943662
45 THP 0.556962 0.971429
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 ATM 0.542169 0.894737
49 TXS 0.538462 0.789474
50 YYY 0.536585 0.891892
51 T3S 0.525 0.789474
52 BVP 0.52381 0.944444
53 ABT 0.521739 0.884615
54 D4D 0.506024 0.928571
55 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 2DT 0.5 0.957747
59 TPE 0.5 0.894737
60 T4K 0.5 0.853659
61 DT ME6 DT 0.5 0.87013
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 DU 0.469136 0.942857
67 UMP 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 DUP 0.449438 0.930556
71 D4T 0.449438 0.928571
72 6U4 0.447917 0.848101
73 ADS THS THS THS 0.444444 0.758621
74 DDN 0.439024 0.942857
75 3DT 0.428571 0.835616
76 UC5 0.425287 0.943662
77 ID2 0.423077 0.8
78 DT MA7 DT 0.420635 0.797619
79 8DG 0.418367 0.829268
80 DUN 0.41573 0.930556
81 5GW 0.410526 0.878378
82 DCM 0.406977 0.878378
83 DC 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 74W 0.4 0.732558
86 74X 0.4 0.732558
87 D4M 0.4 0.914286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1H5T; Ligand: DAU; Similar sites found with APoc: 66
This union binding pocket(no: 1) in the query (biounit: 1h5t.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3QPB URA 1.06383
2 4DFB KAN 1.5528
3 2REG CHT 1.70648
4 5JU6 BGC 2.04778
5 3DUV KDO 2.29008
6 3FXU TSU 2.38908
7 5CGM MAL 2.38908
8 2PEL LBT 2.54237
9 4M3P HCS 2.73038
10 2IRY DGT 2.73038
11 6HL8 GUA 2.73038
12 3FSY SCA 3.07167
13 4NRT 2NG 3.07167
14 5C9P FUC 3.07167
15 3ZDS M8O 3.07167
16 3BRN SRO 3.18471
17 2YQS UD1 3.41297
18 2OEG UPG 3.41297
19 1EYR CDP 3.50877
20 4G86 BNT 3.52113
21 5E9H MLI 3.75427
22 5XK9 DMA 3.87931
23 2ICY UPG 4.09556
24 5CXX FER 4.36364
25 1JV1 UD1 4.43686
26 2NZ2 CIR 4.77816
27 1I52 CTP 5.08475
28 5JIB OIA 5.11945
29 4BHL ARG 5.46075
30 2IF8 ADP 5.46075
31 1AJ8 CIT 5.46075
32 3KIF GDL 5.66038
33 5LV1 78T 5.71429
34 4RP9 ASC 5.80205
35 2FAR DTP 6.14334
36 1L7N ALF 6.63507
37 1L7P SEP 6.63507
38 4URS C2E 6.91489
39 1U6R ADP 7.50853
40 4M0R 644 7.50853
41 5ME4 HP4 7.66423
42 3K8D KDO 7.95455
43 3FJG 3PG 7.96813
44 3OH3 UAD 9.21502
45 3WUC GLC GAL 10.219
46 5EO8 TFU 10.2389
47 1Z6K OAA 10.5802
48 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG 10.9375
49 5OF1 SAL 11.4286
50 1W55 C 11.6041
51 2CI5 HCS 13.0282
52 5LWY OLB 13.3562
53 1DZK PRZ 14.6497
54 1M6P M6P 17.1053
55 1YP4 ADQ 23.8908
56 1YP4 ADP 23.8908
57 4KQL 1SG 30.0341
58 1FWY UD1 30.3754
59 1HV9 UD1 30.3754
60 2X65 M1P 33.3333
61 2PA4 UPG 34.1297
62 4JD0 1KH 37.4502
63 5Z0A NAG 39.2491
64 3JUK UPG 44.8399
65 4Y7U 2KH 47.1861
66 4Y7U 491 47.1861
Pocket No.: 2; Query (leader) PDB : 1H5T; Ligand: DAU; Similar sites found with APoc: 37
This union binding pocket(no: 2) in the query (biounit: 1h5t.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 5C5T AKG 1.75439
2 1FLJ GSH 1.92308
3 1DGH NDP 2.04778
4 5CWA 0GA 2.38908
5 1UH4 GLC 2.38908
6 2JFV FLC 2.4055
7 2PFZ PCA 2.73038
8 1H8P PC 2.75229
9 5KOD IAC 3.07167
10 4IV9 TSR 3.41297
11 2F7A BEZ 3.44828
12 4RGA 3PV 3.75427
13 1ZUW DGL 4.04412
14 1GJW MAL 4.09556
15 5O5Y GLC 4.09556
16 5HWV MBN 4.61538
17 2E0N SAH 4.6332
18 4KJG 4NP 4.77816
19 5VX5 FUC GAL NAG GAL BGC 4.93827
20 5JVB 2PO 6.07143
21 1IXE CIT 6.48464
22 3TIK JKF 6.82594
23 3QMN A3P 6.97674
24 3WBZ ATP 7.01107
25 5LPG 71V 7.31707
26 3K8D CTP 7.95455
27 2DBX GLU 9.55631
28 2BCG GER 9.70874
29 2ZFZ ARG 10.1266
30 1FRW GTP 10.8247
31 1WVC CTP 11.9691
32 2Y6P CTP 12.3932
33 5HS2 CTP 12.5
34 3NOJ PYR 12.605
35 1L0I PSR 20.5128
36 1FTH A3P 26.2295
37 2XWL CTP 26.9058
Pocket No.: 3; Query (leader) PDB : 1H5T; Ligand: TYD; Similar sites found with APoc: 35
This union binding pocket(no: 3) in the query (biounit: 1h5t.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4MFZ MFK 2.38908
2 2D3N GLC GLC GLC 2.73038
3 4KQI RBZ 2.73038
4 4KQI NIO 2.73038
5 1JQ3 AAT 2.73038
6 1JN2 SFP 2.95359
7 1XPJ TLA 3.1746
8 1GPE FAD 3.41297
9 5XFV FMN 3.41297
10 1F76 FMN 3.41297
11 4INB 1F6 3.42466
12 4ELG 52J 3.61446
13 1WUU GLA 3.75427
14 2QE0 NAP 4.09556
15 2ISJ FMN 4.34783
16 1LLU NAD 4.43686
17 5UWS GNP 4.64135
18 5DI9 GNP 4.64135
19 4O8A FAD 4.65793
20 1TIW FAD 5.31561
21 1TIW TFB 5.31561
22 2O66 FLC 6.66667
23 2B6N ALA PRO THR 6.83453
24 1COY FAD 7.16724
25 4NS0 PIO 7.5188
26 4YNU FAD 7.84983
27 6H3O FAD 7.84983
28 3U4C NDP 8.53242
29 3G5N PB2 8.53242
30 4JB1 FAD 8.87372
31 4JB1 NAP 8.87372
32 5OC1 FAD 8.87372
33 2E1A MSE 9.33333
34 1QX4 FAD 15.3285
35 1FQK ALF 17.6871
Pocket No.: 4; Query (leader) PDB : 1H5T; Ligand: TYD; Similar sites found with APoc: 45
This union binding pocket(no: 4) in the query (biounit: 1h5t.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5LJ0 6XX 1.53846
2 2VVM FAD 1.70648
3 3K7M FAD 2.04778
4 2JLD AG1 2.04778
5 5EY0 ILE 2.18978
6 1UUO ORO 2.38908
7 1UUO FMN 2.38908
8 3NRR NAP 2.38908
9 5GVL GI8 2.38908
10 5GVL PLG 2.38908
11 3KJS DQ1 3.07167
12 1LDM NAD 3.07167
13 3RG9 NDP 3.33333
14 3RG9 WRA 3.33333
15 4EHQ GBL 3.37838
16 3WGT FAD 3.41297
17 3WGT QSC 3.41297
18 4ZCC FAD 3.41297
19 5H4S RAM 3.52113
20 4ELG 52I 3.61446
21 4IGH 1EA 3.75427
22 4IGH FMN 3.75427
23 4IGH ORO 3.75427
24 4Z24 FAD 3.75427
25 2R5N TPP 3.75427
26 1OAA OAA 3.861
27 5NMX FAD 4.09556
28 3X0V FAD 4.09556
29 1XXR MAN 4.43686
30 3ITJ FAD 4.77816
31 1D1T NAD 4.77816
32 1RP0 AHZ 4.92958
33 2XVF FAD 5.11945
34 5MZN ADP 5.11945
35 2XVE FAD 5.11945
36 6C74 PC 5.40541
37 4CLI 5P8 6.14334
38 5TDF ADE 7.16724
39 2DT9 THR 7.18563
40 1YY5 FAD 7.50853
41 2YG3 FAD 7.84983
42 5Y6Q MCN 8.64198
43 1CX9 NHP 9.55631
44 5D63 FUC GLA GLA 11.2628
45 2BO4 FLC 13.9932
Pocket No.: 5; Query (leader) PDB : 1H5T; Ligand: DAU; Similar sites found with APoc: 13
This union binding pocket(no: 5) in the query (biounit: 1h5t.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3AJM 4IP None
2 5KY5 GDP 1.70648
3 5W6Y TRP 2.38908
4 2Z48 A2G 2.38908
5 3P7I P7I 2.73038
6 3QXQ CE5 2.73038
7 1BGV GLU 3.41297
8 1NC2 DOE 4.0724
9 3THR C2F 5.80205
10 5KY9 GDP 7.5
11 2C5S AMP 8.87372
12 1I7Q PYR 9.05588
13 2BVE PH5 26.8908
Pocket No.: 6; Query (leader) PDB : 1H5T; Ligand: TYD; Similar sites found with APoc: 33
This union binding pocket(no: 6) in the query (biounit: 1h5t.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4NCW 2KN None
2 4JWH SAH 1.36519
3 1UUO BRF 2.38908
4 3NRR D16 2.38908
5 1TV5 FMN 4.09556
6 4JNA FAD 4.43686
7 4JWF SAH 4.60829
8 3ZH4 FLC 4.77816
9 1WQ1 AF3 4.81928
10 3HQP OXL 5.11945
11 1YJQ NAP 5.11945
12 4NTD FAD 5.46075
13 1NAA 6FA 5.80205
14 1NAA ABL 5.80205
15 5MZY 8EZ 6.41509
16 3AB4 THR 6.74157
17 3QVP FAD 6.82594
18 4WEI GLC GAL 6.85921
19 1COY AND 7.16724
20 3NRZ MTE 7.16724
21 3NRZ HPA 7.16724
22 1FIQ MTE 7.16724
23 1FIQ SAL 7.16724
24 4YNU LGC 7.84983
25 4O08 PO6 8.53242
26 4YSW FAD 8.87372
27 4YSW NAI 8.87372
28 5AE2 FYC 9.55631
29 4LNU GDP 9.55631
30 5KY3 GFB 10
31 1U3U NAD 13.6519
32 1U3U BNF 13.6519
33 3LKF PC 14.6758
Pocket No.: 7; Query (leader) PDB : 1H5T; Ligand: TYD; Similar sites found with APoc: 19
This union binding pocket(no: 7) in the query (biounit: 1h5t.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1MID LAP None
2 2WSB NAD 1.1811
3 3EEL 53T 1.76211
4 1Z83 AP5 2.55102
5 1QF9 C5P 2.57732
6 1QF9 ALF 2.57732
7 1QF9 ADP 2.57732
8 1V97 FAD 3.75427
9 2NXW TPP 3.75427
10 3Q9T FAY 3.75427
11 4OOE FOM 3.75427
12 1IG3 VIB 3.80228
13 5FPE 3TR 4.43686
14 2UXI G50 4.7619
15 2IF8 ADP 5.46075
16 2YKL NLD 6.01852
17 3NRZ FAD 7.16724
18 3WQQ NDP 8.53242
19 3WQQ IB3 8.53242
Pocket No.: 8; Query (leader) PDB : 1H5T; Ligand: DAU; Similar sites found with APoc: 25
This union binding pocket(no: 8) in the query (biounit: 1h5t.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1JQY A32 None
2 2HFN FMN 2.61438
3 1C3M MAN MAN 2.72109
4 4CJN QNZ 2.9595
5 1DNP MHF 3.07167
6 3CV2 COA 3.07167
7 5XQL C2E 3.09278
8 6ACS CIT 3.10078
9 5A0U CHT 3.75427
10 3ALT MLB 3.82166
11 5OCG 9R5 4.2328
12 2NZ2 ASP 4.77816
13 4A38 BZS 4.77816
14 1ONI BEZ 5.07246
15 4URG C2E 5.98802
16 2W5P CL8 6.71141
17 5WL1 CUY 6.82594
18 4DDY DN6 6.84411
19 1H7F C5P 6.93878
20 2VOH CIT 7.64331
21 5H9P TD2 8.86076
22 4WOE 3S5 8.87372
23 2H7C SIA 8.87372
24 1LES GLC FRU 11.0497
25 1P7T PYR 12.9693
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