Receptor
PDB id Resolution Class Description Source Keywords
4D0Z 2.2 Å EC: 2.4.1.41 GALNAC-T2 CRYSTAL SOAKED WITH UDP-5SGALNAC, MEA2 AND MANGANESE (HIGHER RESOLUTION DATASET) HOMO SAPIENS TRANSFERASE-PEPTIDE COMPLEX RETAINING GALNAC-T2 SUBSTRATE-SNI-TYPE REACTION QM/MM METADYNAMICS BI-BI KINETIC MECHANSUBSTRATE SPECIFICITY ACETAMIDO GROUP
Ref.: SUBSTRATE-GUIDED FRONT-FACE REACTION REVEALED BY CO STRUCTURAL SNAPSHOTS AND METADYNAMICS FOR THE POLYP N- ACETYLGALACTOSAMINYLTRANSFERASE 2. ANGEW.CHEM.INT.ED.ENGL. V. 53 8206 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1580;
B:1576;
B:1573;
D:1575;
A:1577;
A:1574;
A:1575;
E:1572;
E:1579;
E:1582;
E:1570;
E:1581;
A:1572;
A:1579;
E:1577;
A:1571;
D:1573;
B:1578;
E:1573;
E:1576;
E:1578;
D:1576;
A:1573;
E:1583;
B:1572;
A:1576;
E:1574;
B:1577;
D:1577;
B:1574;
E:1580;
E:1571;
E:1575;
B:1575;
A:1578;
D:1574;
B:1579;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN E:1586;
D:1570;
A:1570;
C:1570;
F:1570;
B:1570;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
SER THR CYS PRO ALA ALA X:5;
Y:5;
Valid;
Valid;
none;
none;
submit data
478.571 n/a SCC(N...
HWU E:1585;
B:1571;
A:1582;
D:1571;
F:1571;
C:1569;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
623.419 C17 H27 N3 O16 P2 S CC(=O...
BBK D:1572;
A:1581;
E:1584;
B:1580;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
237.273 C8 H15 N O5 S CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FV9 2.07 Å EC: 2.4.1.41 CRYSTAL STRUCTURE OF GALNAC-T2 IN COMPLEX WITH COMPOUND 16D HOMO SAPIENS TRANSFERASE
Ref.: GLYCOMIMETICS TARGETING GLYCOSYLTRANSFERASES: SYNTH COMPUTATIONAL AND STRUCTURAL STUDIES OF LESS-POLAR CONJUGATES. CHEMISTRY V. 22 7215 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SER THR CYS PRO ALA ALA; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 SER THR CYS PRO ALA ALA 1 1
2 SER GLU CYS THR THR PRO CYS 0.533981 0.964912
3 SER SER CYS PRO LEU SER LYS 0.481132 0.931035
4 SER ALA PRO ASP THR ARG PRO ALA 0.478632 0.80597
5 SER VAL PRO ILE 0.462366 0.847458
6 SER TYR SER PRO THR SEP PRO SER 0.461538 0.828125
7 ALA PRO ASP THR ARG PRO ALA PRO 0.452174 0.791045
8 CYS THR PRO SER ARG 0.436364 0.857143
9 ASP SER THR THR PRO ALA PRO THR 0.43299 0.862069
10 LYS LEU THR PRO LEU CYS VAL THR LEU 0.432203 0.915254
11 ALA ASN SER ARG LEU PRO THR SER ILE ILE 0.425926 0.915254
12 ARG VAL ALA SER PRO THR SER GLY VAL 0.422764 0.830769
13 ARG VAL SER PRO SER THR SER TYR THR PRO 0.422414 0.885246
14 TYR SEP PRO THR SEP PRO SER 0.422414 0.768116
15 01B PRO PRO ALA NH2 0.421569 0.770492
16 PRO SER TYR SEP PRO THR SEP PRO SER 0.420561 0.8125
17 GLY THR SER SER PRO SER ALA ASP 0.418182 0.947368
18 ALA PRO THR 0.416667 0.824561
19 ALA THR PRO PHE GLN GLU 0.415842 0.877193
20 ASN LEU VAL PRO SER VAL ALA THR VAL 0.408333 0.885246
21 ARG ARG ARG GLU ARG SER PRO THR ARG 0.406504 0.815385
22 SER THR SEP PRO THR PHE ASN LYS 0.405797 0.794118
23 LEU PRO GLU THR GLY 0.40566 0.881356
24 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.403226 0.818182
25 ALA VAL PRO ALA 0.4 0.754386
Ligand no: 2; Ligand: HWU; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 HWU 1 1
2 12V 1 1
3 UD2 0.660377 0.943662
4 UD1 0.660377 0.943662
5 HP7 0.633027 0.929577
6 UD7 0.618182 0.916667
7 MJZ 0.612613 0.90411
8 UDM 0.611111 0.930556
9 UD4 0.607143 0.90411
10 UDZ 0.6 0.846154
11 UFM 0.592233 0.929577
12 GDU 0.592233 0.929577
13 GUD 0.592233 0.929577
14 UPG 0.592233 0.929577
15 EPZ 0.589744 0.930556
16 EEB 0.584746 0.917808
17 EPU 0.584746 0.917808
18 UGB 0.579439 0.915493
19 UGA 0.579439 0.915493
20 UDP 0.578947 0.901408
21 UTP 0.57732 0.901408
22 UDX 0.560748 0.902778
23 UPF 0.560748 0.88
24 UAD 0.560748 0.902778
25 UFG 0.560748 0.88
26 U2F 0.560748 0.88
27 UNP 0.56 0.876712
28 USQ 0.550459 0.814815
29 UMA 0.547619 0.930556
30 URM 0.54717 0.916667
31 660 0.54717 0.916667
32 3UC 0.540541 0.88
33 U22 0.534351 0.807229
34 UPU 0.533981 0.928571
35 G3N 0.531532 0.878378
36 UPP 0.523364 0.902778
37 UDH 0.523364 0.833333
38 U21 0.522727 0.82716
39 U20 0.522727 0.82716
40 U5P 0.515789 0.887324
41 UDP UDP 0.515152 0.873239
42 44P 0.5 0.864865
43 UAG 0.496454 0.881579
44 2KH 0.495146 0.876712
45 IUG 0.491803 0.783133
46 4RA 0.478873 0.825
47 UDP GAL 0.477876 0.902778
48 UD0 0.472222 0.814815
49 UP5 0.472 0.822785
50 UML 0.467105 0.82716
51 Y6W 0.460177 0.88
52 4TC 0.453125 0.802469
53 U U 0.431034 0.888889
54 2QR 0.429577 0.817073
55 PMP UD1 0.427586 0.790123
56 U 0.425532 0.828571
57 URI 0.425532 0.828571
58 U3P 0.415842 0.873239
59 UA3 0.415842 0.873239
60 CSQ 0.414634 0.893333
61 CSV 0.414634 0.893333
62 CJB 0.412371 0.814286
63 C5G 0.411765 0.88
Ligand no: 3; Ligand: BBK; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 0YT 1 1
2 BBK 1 1
3 GLT 0.439024 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5fv9.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5FV9; Ligand: Y6W; 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: 5fv9.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5fv9.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5FV9; Ligand: UDP; 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: 5fv9.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: 15
This union binding pocket(no: 5) in the query (biounit: 5fv9.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JCM ISD 0.01248 0.41773 2.88248
2 3CU0 UDP 0.0001104 0.44316 3.55872
3 3CU0 GAL GAL SO4 0.000897 0.44017 3.55872
4 3U2U UDP 0.002009 0.42567 3.80228
5 3CKJ CIT 0.01708 0.40708 4.25532
6 4YDD MGD 0.0116 0.42271 5.77933
7 4YDD MD1 0.0116 0.42271 5.77933
8 2BVL GLC 0.003618 0.40208 5.89319
9 2BVL UDP 0.003618 0.40208 5.89319
10 4M4K XYP XYP 0.001494 0.41067 6.62021
11 4M4K GDU 0.001494 0.41067 6.62021
12 1OMZ UD2 0.00003811 0.46472 7.16724
13 2APC UDM 0.001998 0.4029 7.60234
14 5MM0 GDD 0.000432 0.44208 13.1016
15 5TZJ UD1 0.00000559 0.52592 13.587
Pocket No.: 6; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5fv9.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5fv9.bio4) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5FV9; Ligand: Y6W; 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: 5fv9.bio4) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5fv9.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5fv9.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: 8
This union binding pocket(no: 11) in the query (biounit: 5fv9.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VL8 CTS 0.001704 0.40437 2.9304
2 2VL8 UDP 0.002223 0.40343 2.9304
3 3OID NDP 0.008984 0.40255 3.87597
4 5UQK U2F 0.004224 0.40375 4.30108
5 2AGD NAG MAN BMA 0.002728 0.41919 6.96864
6 2AGD UDH 0.002946 0.41919 6.96864
7 4DEC UDP 0.01786 0.40867 8.43023
8 4DEC 3PG 0.01786 0.40867 8.43023
Pocket No.: 12; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: 20
This union binding pocket(no: 12) in the query (biounit: 5fv9.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VL8 CTS 0.001704 0.40437 2.9304
2 2VL8 UDP 0.002223 0.40343 2.9304
3 3CU0 UDP 0.0002669 0.43657 3.55872
4 3CU0 GAL GAL SO4 0.00144 0.43495 3.55872
5 3U2U UDP 0.001107 0.43977 3.80228
6 3OID NDP 0.008984 0.40255 3.87597
7 3CKJ CIT 0.01252 0.4157 4.25532
8 5UQK U2F 0.004224 0.40375 4.30108
9 2BVL UDP 0.002774 0.41116 5.89319
10 2BVL GLC 0.002774 0.41116 5.89319
11 4M4K XYP XYP 0.0009451 0.42279 6.62021
12 4M4K GDU 0.0009451 0.42279 6.62021
13 2AGD NAG MAN BMA 0.002728 0.41919 6.96864
14 2AGD UDH 0.002946 0.41919 6.96864
15 1OMZ UD2 0.00004281 0.47132 7.16724
16 2APC UDM 0.0007151 0.42401 7.60234
17 4DEC UDP 0.01786 0.40867 8.43023
18 4DEC 3PG 0.01786 0.40867 8.43023
19 5MM0 GDD 0.0003503 0.44949 13.1016
20 5TZJ UD1 0.000003119 0.54159 13.587
Pocket No.: 13; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 5fv9.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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