Receptor
PDB id Resolution Class Description Source Keywords
4HN1 1.6 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF H60N/Y130F DOUBLE MUTANT OF CHMJ, A 3'- MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH STREPTOMYCES BIKINIENSIS 3-prime -MONOEPIMERASE NATURAL PRODUCT DEOXYSUGAR CHALCOMYCIN MYCINOSE CUPIN FOLD NUCLEOTIDE-LINKED SUGAR EPIMERIZATIOUNKNOWN FUNCTION
Ref.: STRUCTURAL AND FUNCTIONAL STUDIES ON A 3'-EPIMERASE IN THE BIOSYNTHESIS OF DTDP-6-DEOXY-D-ALLOSE. BIOCHEMISTRY V. 51 9375 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:301;
A:302;
A:303;
A:304;
B:301;
B:302;
B:303;
C:301;
C:302;
D:301;
D:302;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
TDR C:305;
D:303;
Valid;
Valid;
none;
none;
submit data
126.113 C5 H6 N2 O2 CC1=C...
THM A:306;
B:305;
Valid;
Valid;
none;
none;
submit data
242.229 C10 H14 N2 O5 CC1=C...
TYD A:305;
B:304;
C:303;
C:304;
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
4HN1 1.6 Å EC: 5.-.-.- CRYSTAL STRUCTURE OF H60N/Y130F DOUBLE MUTANT OF CHMJ, A 3'- MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH STREPTOMYCES BIKINIENSIS 3-prime -MONOEPIMERASE NATURAL PRODUCT DEOXYSUGAR CHALCOMYCIN MYCINOSE CUPIN FOLD NUCLEOTIDE-LINKED SUGAR EPIMERIZATIOUNKNOWN FUNCTION
Ref.: STRUCTURAL AND FUNCTIONAL STUDIES ON A 3'-EPIMERASE IN THE BIOSYNTHESIS OF DTDP-6-DEOXY-D-ALLOSE. BIOCHEMISTRY V. 51 9375 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4HN1 - TDR C5 H6 N2 O2 CC1=CNC(=O....
2 4HMZ - 18T C16 H26 N2 O15 P2 C[C@@H]1[C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 24 families.
1 4HN1 - TDR C5 H6 N2 O2 CC1=CNC(=O....
2 4HMZ - 18T C16 H26 N2 O15 P2 C[C@@H]1[C....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1OI6 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
2 4HN1 - TDR C5 H6 N2 O2 CC1=CNC(=O....
3 4HMZ - 18T C16 H26 N2 O15 P2 C[C@@H]1[C....
4 2IXC - TRH C16 H26 N2 O15 P2 C[C@H]1[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TDR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 TDR 1 1
2 IUR 0.483871 0.860465
3 WBU 0.451613 0.840909
4 URF 0.451613 0.860465
5 5UC 0.4375 0.860465
6 FYU 0.4 0.95
Ligand no: 2; Ligand: THM; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 THM 1 1
2 LLT 1 1
3 0DN 0.777778 0.923077
4 TXS 0.704918 0.869565
5 TMP 0.693548 0.859155
6 T3S 0.68254 0.869565
7 TYD 0.641791 0.873239
8 ID2 0.637931 0.910448
9 T3P 0.629032 0.84507
10 TBD 0.623188 0.837838
11 AZZ 0.609375 0.857143
12 TTP 0.605634 0.873239
13 BVD 0.587302 0.953846
14 BTD 0.550725 0.873239
15 3DT 0.540984 0.953846
16 FDM 0.536232 0.8
17 NYM 0.536232 0.835616
18 THP 0.528571 0.84507
19 WMJ 0.525 0.78481
20 DAU 0.52381 0.863014
21 TLO 0.518519 0.849315
22 ATM 0.513514 0.779221
23 DUR 0.508197 0.952381
24 0TT 0.506494 0.926471
25 DT DT DT 0.5 0.833333
26 3YN 0.5 0.837838
27 3R2 0.494118 0.826667
28 TDX 0.494118 0.849315
29 18T 0.494118 0.837838
30 1JB 0.494118 0.837838
31 TRH 0.494118 0.837838
32 MCY 0.492308 0.925373
33 74W 0.488636 0.775
34 74X 0.488636 0.775
35 DT DT DT DT DT 0.488372 0.824324
36 ATY 0.487179 0.824324
37 T3F 0.482759 0.815789
38 T3Q 0.482759 0.815789
39 DWN 0.482759 0.815789
40 5HU 0.478873 0.873239
41 T46 0.477273 0.837838
42 0N2 0.477273 0.805195
43 AZD 0.475 0.792208
44 DT DT PST 0.47191 0.813333
45 MMF 0.47191 0.815789
46 0FX 0.47191 0.815789
47 UFP 0.464789 0.786667
48 2DT 0.463768 0.833333
49 QDM 0.461538 0.805195
50 BRU 0.458333 0.786667
51 AKM 0.456522 0.775
52 FNF 0.456522 0.826667
53 1YF 0.456522 0.826667
54 JHZ 0.456522 0.794872
55 5IU 0.452055 0.786667
56 4TG 0.451613 0.826667
57 BVP 0.435897 0.821918
58 T5A 0.431373 0.756098
59 TMC 0.426471 0.882353
60 ABT 0.425287 0.772152
61 DCZ 0.424242 0.880597
62 LDC 0.424242 0.880597
63 QUH 0.42 0.815789
64 FUH 0.42 0.815789
65 4TA 0.419048 0.743902
66 D3T 0.417722 0.847222
67 DT ME6 DT 0.415842 0.802632
68 5MD 0.411765 0.953125
69 ADS THS THS THS 0.411215 0.746988
70 DPB 0.407407 0.783784
71 TPE 0.406593 0.802632
72 B86 0.405797 0.84507
73 5BT 0.405797 0.84507
Ligand no: 3; Ligand: TYD; Similar ligands found: 88
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 18T 0.682353 0.932432
7 TDX 0.682353 0.945205
8 3R2 0.682353 0.92
9 1JB 0.682353 0.932432
10 TRH 0.682353 0.932432
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3F 0.666667 0.907895
15 T3Q 0.666667 0.907895
16 TBD 0.662338 0.958904
17 0N2 0.659091 0.896104
18 T46 0.659091 0.932432
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 LLT 0.641791 0.873239
23 THM 0.641791 0.873239
24 QDM 0.637363 0.896104
25 AKM 0.630435 0.886076
26 FNF 0.630435 0.92
27 JHZ 0.630435 0.884615
28 1YF 0.630435 0.92
29 4TG 0.623656 0.92
30 DUD 0.61039 0.957143
31 0DN 0.6 0.833333
32 UFP 0.6 0.905405
33 DT DT DT DT DT 0.582418 0.945205
34 QUH 0.58 0.907895
35 FUH 0.58 0.907895
36 T5A 0.572816 0.841463
37 5HU 0.571429 0.971831
38 BRU 0.571429 0.905405
39 FDM 0.564103 0.918919
40 NYM 0.564103 0.958333
41 5IU 0.564103 0.905405
42 DT DT PST 0.56383 0.881579
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 TXS 0.538462 0.789474
49 YYY 0.536585 0.891892
50 T3S 0.525 0.789474
51 BVP 0.52381 0.944444
52 ABT 0.521739 0.884615
53 DT DT DT 0.511364 0.878378
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 TPE 0.5 0.894737
59 DT ME6 DT 0.5 0.87013
60 T4K 0.5 0.853659
61 2DT 0.5 0.957747
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 UMP 0.469136 0.942857
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 D4T 0.449438 0.928571
71 DUP 0.449438 0.930556
72 6U4 0.447917 0.848101
73 DDN 0.439024 0.942857
74 3DT 0.428571 0.835616
75 UC5 0.425287 0.943662
76 ID2 0.423077 0.8
77 DT MA7 DT 0.420635 0.797619
78 8DG 0.418367 0.829268
79 DUN 0.41573 0.930556
80 DUT MG 0.413043 0.864865
81 5GW 0.410526 0.878378
82 DC 0.406977 0.878378
83 DCM 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 ADS THS THS THS 0.403361 0.767442
86 74W 0.4 0.732558
87 D4M 0.4 0.914286
88 74X 0.4 0.732558
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4HN1; Ligand: TYD; Similar sites found: 53
This union binding pocket(no: 1) in the query (biounit: 4hn1.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2QO4 CHD 0.008024 0.43068 None
2 5FU3 BGC BGC BGC 0.01541 0.40289 None
3 4QPW XYP XYP XYP 0.0002287 0.4985 1.40845
4 1Y0G 8PP 0.04596 0.40407 2.09424
5 4JHG ZEA 0.006626 0.41649 2.38095
6 1GP6 QUE 0.003085 0.44714 2.48756
7 1GP6 SIN 0.003254 0.4444 2.48756
8 2XMY CDK 0.03771 0.42144 2.48756
9 2FUE M1P 0.001566 0.40449 2.48756
10 5JNN 6LM 0.006869 0.42676 2.63158
11 3OJI PYV 0.01494 0.4052 2.6455
12 4WVW SLT 0.0007095 0.47927 2.77778
13 3NMV PYV 0.006832 0.41585 2.80899
14 1XE7 GUN 0.009074 0.40841 2.98507
15 4MLO PAM 0.01014 0.40554 2.98507
16 4D06 NAR 0.01678 0.40442 2.98507
17 2A1L PCW 0.002982 0.46753 3.48259
18 4RFR RHN 0.005539 0.42428 3.48259
19 2EPN NGT 0.01619 0.40062 3.48259
20 2PA7 TYD 0.000007095 0.51038 3.5461
21 3MI2 PFU 0.01403 0.43645 3.9801
22 2ET1 GLV 0.005817 0.42349 4.47761
23 4MP8 NAD 0.03842 0.40464 4.47761
24 3MTX PGT 0.03145 0.40296 4.63576
25 3JRS A8S 0.0145 0.40753 4.80769
26 1ZB6 GST 0.01699 0.41421 4.97512
27 1MJJ HAL 0.01827 0.40723 4.97512
28 5TPU TYD 0.0001057 0.50983 5.03597
29 1ODM ASV 0.01299 0.4146 5.47264
30 4WOE ADP 0.01423 0.40555 5.97015
31 3Q8G PEE 0.03679 0.41689 6.46766
32 3VQ2 LP4 LP5 MYR DAO 0.01869 0.42477 6.94444
33 4W9N TCL 0.01454 0.40577 6.96517
34 5TVM PUT 0.007488 0.42326 7.05882
35 5T7I LAT NAG GAL 0.006174 0.42403 7.09677
36 3SAO NKN 0.004639 0.41681 7.5
37 1T27 PCW 0.01517 0.42954 7.9602
38 1KTG AMP 0.0181 0.40018 8.69565
39 1J3R 6PG 0.005635 0.41287 8.94737
40 3W9R A8S 0.006599 0.4121 8.95522
41 5JO1 6LM 0.01664 0.40292 8.95522
42 3G08 FEE 0.04133 0.41414 9.45274
43 3QRC SCR 0.008217 0.42325 9.55414
44 5U98 1KX 0.01945 0.42204 10.101
45 5F3I 5UJ 0.02837 0.40166 10.4478
46 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 0.006519 0.42086 12.4378
47 4MZU TYD 0.00002101 0.5464 12.5
48 5A3T MMK 0.005212 0.44146 14.9254
49 4ZU5 THM 0.00006567 0.51194 20.1389
50 1NYW DAU 0.000000009123 0.70294 40.1015
51 1DZT TPE 0.00000007406 0.67766 44.8087
52 1DZT ATY 0.0000001053 0.66772 44.8087
53 1EPZ TYD 0.00002244 0.49231 48.6486
Pocket No.: 2; Query (leader) PDB : 4HN1; Ligand: THM; 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: 4hn1.bio1) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4HN1; Ligand: THM; Similar sites found: 2
This union binding pocket(no: 3) in the query (biounit: 4hn1.bio1) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MGB GHP 3MY 3FG GHP GHP OMY 3FG 0.04609 0.4225 2.98507
2 1KQ4 FAD 0.00005396 0.56888 11.2069
Pocket No.: 4; Query (leader) PDB : 4HN1; Ligand: TYD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4hn1.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4HN1; Ligand: TDR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4hn1.bio2) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4HN1; Ligand: TYD; Similar sites found: 13
This union binding pocket(no: 6) in the query (biounit: 4hn1.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LN1 DLP 0.01321 0.41572 2.48756
2 4Y24 TD2 0.01217 0.40178 3.24675
3 1DRJ RIP 0.02113 0.40101 4.97512
4 5H9Q TD2 0.01094 0.40552 7.09677
5 3ZXE PGZ 0.0006573 0.40327 8.27068
6 5JSP DQY 0.01413 0.40897 8.95522
7 4FFG 0U8 0.004627 0.43655 9.95025
8 4RYV ZEA 0.01228 0.40158 10.3226
9 4YRD 3IT 0.01176 0.41957 10.4478
10 1ULE GLA GAL NAG 0.02051 0.40265 11.3333
11 5W0N UPU 0.01656 0.40386 13.9303
12 1JGS SAL 0.0241 0.41427 15.2174
13 5KEW 6SB 0.02097 0.40187 18.0556
Pocket No.: 7; Query (leader) PDB : 4HN1; Ligand: TDR; Similar sites found: 2
This union binding pocket(no: 7) in the query (biounit: 4hn1.bio2) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KQ4 FAD 0.00005052 0.57695 11.2069
2 3L8W XAN 0.005347 0.40438 13.4328
Pocket No.: 8; Query (leader) PDB : 4HN1; Ligand: TYD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4hn1.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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