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Receptor
PDB id Resolution Class Description Source Keywords
3OTH 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CALG1, CALICHEAMICIN GLYCOSTYLTRANSFERA AND CALICHEAMICIN ALPHA3I BOUND FORM MICROMONOSPORA ECHINOSPORA CALICHEAMICIN TDP STRUCTURAL GENOMICS PSI-2 PROTEIN STRUINITIATIVE CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS CESGFOLD GLYCOSYLTRANSFERASE TRANSFERASE-ANTIBIOTIC COMPLEX DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS NATPRO
Ref.: COMPLETE SET OF GLYCOSYLTRANSFERASE STRUCTURES IN T CALICHEAMICIN BIOSYNTHETIC PATHWAY REVEALS THE ORIG REGIOSPECIFICITY. PROC.NATL.ACAD.SCI.USA V. 108 17649 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CLJ A:394;
B:394;
Valid;
Valid;
none;
none;
submit data
1211.14 C47 H59 I N2 O19 S4 Cc1c(...
TYD A:393;
B:393;
Valid;
Valid;
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
3OTH 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CALG1, CALICHEAMICIN GLYCOSTYLTRANSFERA AND CALICHEAMICIN ALPHA3I BOUND FORM MICROMONOSPORA ECHINOSPORA CALICHEAMICIN TDP STRUCTURAL GENOMICS PSI-2 PROTEIN STRUINITIATIVE CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS CESGFOLD GLYCOSYLTRANSFERASE TRANSFERASE-ANTIBIOTIC COMPLEX DISCOVERY FOR NATURAL PRODUCT BIOSYNTHESIS NATPRO
Ref.: COMPLETE SET OF GLYCOSYLTRANSFERASE STRUCTURES IN T CALICHEAMICIN BIOSYNTHETIC PATHWAY REVEALS THE ORIG REGIOSPECIFICITY. PROC.NATL.ACAD.SCI.USA V. 108 17649 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3OTH - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 3OTG - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3OTH - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 3OTG - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3OTH - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
2 3OTG - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CLJ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 CLJ 1 1
2 C0T 0.584416 0.864198
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 : 3OTH; Ligand: CLJ; Similar sites found with APoc: 24
This union binding pocket(no: 1) in the query (biounit: 3oth.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3KP6 SAL 1.94175
2 6CGN DA 2.18447
3 1OFZ FUC 2.24359
4 1OFZ FUL 2.24359
5 4MGD 27N 3.13725
6 2BJ4 OHT 3.1746
7 5AAV GW5 3.1746
8 3UU7 2OH 3.18725
9 3UUA 0CZ 3.18725
10 2E2R 2OH 3.27869
11 2ZXI FAD 3.64078
12 2WQ4 SFU 3.84615
13 1B09 PC 3.8835
14 2I0G I0G 5.05837
15 2YJD YJD 5.41667
16 3OLL EST 5.41667
17 4OIV XX9 7.9646
18 3SAO DBH 8.125
19 5LX9 OLB 10.5634
20 5UGW GSH 13.7143
21 2Y69 CHD 18.75
22 5Z84 CHD 25.4237
23 5W97 CHD 25.4237
24 5ZCO CHD 25.4237
Pocket No.: 2; Query (leader) PDB : 3OTH; Ligand: TYD; Similar sites found with APoc: 83
This union binding pocket(no: 2) in the query (biounit: 3oth.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1FWV SGA MAG FUC None
2 2VK4 TPP 1.45631
3 1Q19 SSC 1.94175
4 5TWB FAD 2.03488
5 1PS9 FAD 2.18447
6 3EYA TDP 2.18447
7 4TXJ THM 2.36486
8 4MO2 FDA 2.44565
9 2HIM ASN 2.51397
10 2C6Q NDP 2.5641
11 1ZPD DPX 2.6699
12 2A2C ADP 2.6699
13 2A2C NG1 2.6699
14 5NV8 TRH 2.82051
15 2AWN ADP 2.88714
16 1T9D P22 2.91262
17 5WS9 AMP 2.91262
18 1IZC PYR 2.94985
19 3HBN UDP 3.19149
20 1W6F ISZ 3.23741
21 5NC9 8SZ 3.23887
22 3Q9T FAY 3.39806
23 2GEK GDP 3.44828
24 5LQ8 GB 3.5461
25 4C3Y FAD 3.58491
26 4C3Y ANB 3.58491
27 3AB1 FAD 3.61111
28 1G6H ADP 3.89105
29 5NE2 DGL 3.95683
30 2NXW TPP 4.12621
31 3GF4 FAD 4.35897
32 4ZOH FAD 4.85437
33 4L80 OXL 4.88506
34 6BK3 UDP 5.33981
35 4GYW UDP 5.33981
36 6MA3 JAJ 5.33981
37 5BNW 12V 5.33981
38 4N3A UDP 5.33981
39 1V7Z CRN 5.33981
40 5EXE 5SR 5.41401
41 1NVM NAD 5.50725
42 3BEO UDP 5.6
43 1V59 FAD 5.82524
44 2C1X UDP 6.06796
45 4X1T UDP 6.06796
46 1MJH ATP 6.17284
47 5XVS UDP 6.33245
48 5ZI9 FLC 6.53846
49 1JJ7 ADP 6.53846
50 3BY9 SIN 6.53846
51 5OLK DTP 6.5534
52 3HRD MCN 6.66667
53 2VCH UDP 7.03884
54 1QPB PYM 7.28155
55 1QPB TPP 7.28155
56 2Q8Z NUP 8.18713
57 4U00 ADP 8.19672
58 5UAO FAD 8.25243
59 5AJU RP5 8.39416
60 4PQG UDP 8.73786
61 3IAE D7K 8.73786
62 2P3V SRT 8.98438
63 3HQP OXL 9.2233
64 2ACV UDP 9.46602
65 1PVN MZP 9.46602
66 5NM7 GLY 10.1504
67 3H4T UDP 12.1359
68 5ENZ UDP 12.7273
69 2IV3 UDP 12.8641
70 2VBF TPP 13.1068
71 4HZ0 1AV 13.1455
72 5V2J UDP 15.7767
73 5V2J 7WV 15.7767
74 3S2U UD1 16.4384
75 1RRV TYD 20.3883
76 3HBF UDP 23.0583
77 3HBF MYC 23.0583
78 4PU6 ASP 23.6641
79 1NLM UD1 34.7087
80 2IYF UDP 36.165
81 2IYA UDP 40.7767
82 3UYK 0CX 40.7767
83 4RIF 3R2 49.6042
Pocket No.: 3; Query (leader) PDB : 3OTH; Ligand: CLJ; Similar sites found with APoc: 57
This union binding pocket(no: 3) in the query (biounit: 3oth.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 2JC9 ADN 1.69903
2 1XI9 PLP 1.72414
3 2ABJ CBC 2.18579
4 3H0A 9RA 2.20588
5 5DT6 GLU 2.24719
6 2HIM ASN 2.51397
7 5NV8 TRH 2.82051
8 1NHZ 486 2.85714
9 2AWN ADP 2.88714
10 1T9D P22 2.91262
11 1G8S MET 3.04348
12 4MGB XDH 3.13725
13 3HBN UDP 3.19149
14 1I0B PEL 3.31325
15 4TQK NAG 3.44828
16 2GEK GDP 3.44828
17 5LQ8 GB 3.5461
18 1YBH P22 3.8835
19 4B5W PYR 3.90625
20 4Q0P 0MK 4.23077
21 5JVB 2PO 4.64286
22 2UXI G50 4.7619
23 4OAR 2S0 5.03876
24 6BK3 UDP 5.33981
25 3BEO UDP 5.6
26 4R57 ACO 5.68182
27 4X1T UDP 6.06796
28 2C1X UDP 6.06796
29 5XVS UDP 6.33245
30 5ZI9 FLC 6.53846
31 1JJ7 ADP 6.53846
32 5OLK DTP 6.5534
33 2VCH UDP 7.03884
34 1DKF BMS 7.65957
35 4PQG UDP 8.73786
36 2P3V SRT 8.98438
37 3HQP OXL 9.2233
38 2ACV UDP 9.46602
39 2GOO NDG 9.64912
40 5W7B MYR 9.92908
41 5NM7 GLY 10.1504
42 3H4T UDP 12.1359
43 1NU4 MLA 12.3711
44 5ENZ UDP 12.7273
45 2IV3 UDP 12.8641
46 4HZ0 1AV 13.1455
47 5V2J UDP 15.7767
48 5V2J 7WV 15.7767
49 3S2U UD1 16.4384
50 1RRV TYD 20.3883
51 3HBF UDP 23.0583
52 3HBF MYC 23.0583
53 3ZCB ATP 32.2581
54 1NLM UD1 34.7087
55 2IYF UDP 36.165
56 2IYA UDP 40.7767
57 4RIF 3R2 49.6042
Pocket No.: 4; Query (leader) PDB : 3OTH; Ligand: TYD; Similar sites found with APoc: 20
This union binding pocket(no: 4) in the query (biounit: 3oth.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2C42 PYR 1.29976
2 2C42 TPP 1.29976
3 2WET FAD 1.69903
4 4MO2 FAD 2.44565
5 2C7G FAD 2.91262
6 2C7G ODP 2.91262
7 1I8T FAD 3.26975
8 4RPL 3UC 3.7594
9 1YBH P22 3.8835
10 5TCI MLI 3.90244
11 4B5W PYR 3.90625
12 5E5U MLI 4.0201
13 3GF4 UPG 4.35897
14 1V97 MTE 4.61165
15 4L9Z OXL 5.01475
16 2UZ1 TPP 8.73786
17 2GOO NDG 9.64912
18 1FIQ MTE 10.9589
19 4IXH IMP 11.0803
20 3NRZ HPA 14.0244
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