-->
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
5NDF 2.3 Å EC: 2.4.1.41 SMALL-MOLECULE INHIBITION OF PPGALNAC-TS SELECTIVELY REDUCES TYPE O-GLYCOSYLATION HOMO SAPIENS GALNAC-T2 INHIBITION FLAVONOIDS MUCIN-TYPE O-GLYCOSYLATION ADISEASE TRANSFERASE
Ref.: THE SMALL MOLECULE LUTEOLIN INHIBITS N-ACETYL-ALPHA-GALACTOSAMINYLTRANSFERASES AND REDUC MUCIN-TYPE O-GLYCOSYLATION OF AMYLOID PRECURSOR PRO J. BIOL. CHEM. V. 292 21304 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 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: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 SER THR CYS PRO ALA ALA 1 1
2 SER GLU CYS THR THR PRO CYS 0.514286 0.965517
3 SER ALA PRO ASP THR ARG PRO ALA 0.470588 0.820895
4 SER VAL PRO ILE 0.467391 0.883333
5 SER SER CYS PRO LEU SER LYS 0.454545 0.932203
6 SER TYR SER PRO THR SEP PRO SER 0.451923 0.830769
7 ARG VAL SER PRO SER THR SER TYR THR PRO 0.451327 0.887097
8 ALA PRO ASP THR ARG PRO ALA PRO 0.448276 0.80597
9 ASP SER THR THR PRO ALA PRO THR 0.447917 0.864407
10 CYS THR PRO SER ARG 0.445455 0.873016
11 TYR SEP PRO THR SEP PRO SER 0.434783 0.771429
12 ALA PRO THR 0.433735 0.827586
13 ALA THR PRO PHE GLN GLU 0.43 0.87931
14 ALA VAL PRO ALA 0.41573 0.775862
15 LYS LEU THR PRO LEU CYS VAL THR LEU 0.413223 0.916667
16 ARG VAL ALA SER PRO THR SER GLY VAL 0.41129 0.846154
17 TYR LEU GLU PRO ALA PRO VAL THR ALA 0.40625 0.791045
18 GLY THR SER SER PRO SER ALA ASP 0.405405 0.931035
19 MET CYS PRO ARG MET THR ALA VAL MET 0.402985 0.797101
Ligand no: 2; Ligand: HWU; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 12V 1 1
2 HWU 1 1
3 UD1 0.660377 0.943662
4 UD2 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 F5P 0.607143 0.90411
10 UD4 0.607143 0.90411
11 F5G 0.607143 0.916667
12 UDZ 0.6 0.846154
13 GUD 0.592233 0.929577
14 UPG 0.592233 0.929577
15 GDU 0.592233 0.929577
16 UFM 0.592233 0.929577
17 EPZ 0.589744 0.930556
18 EEB 0.584746 0.917808
19 EPU 0.584746 0.917808
20 UGA 0.579439 0.915493
21 UGB 0.579439 0.915493
22 UDP 0.578947 0.901408
23 UTP 0.57732 0.901408
24 UAD 0.560748 0.902778
25 UPF 0.560748 0.88
26 UDX 0.560748 0.902778
27 UFG 0.560748 0.88
28 U2F 0.560748 0.88
29 UNP 0.56 0.876712
30 USQ 0.550459 0.814815
31 UMA 0.547619 0.930556
32 URM 0.54717 0.916667
33 660 0.54717 0.916667
34 3UC 0.540541 0.88
35 U22 0.534351 0.807229
36 UPU 0.533981 0.928571
37 G3N 0.531532 0.878378
38 UPP 0.523364 0.902778
39 UDH 0.523364 0.833333
40 U21 0.522727 0.82716
41 U20 0.522727 0.82716
42 U5P 0.515789 0.887324
43 U 0.515789 0.887324
44 UDP UDP 0.515152 0.873239
45 44P 0.5 0.864865
46 UAG 0.496454 0.881579
47 2KH 0.495146 0.876712
48 IUG 0.491803 0.783133
49 4RA 0.478873 0.825
50 UD0 0.472222 0.814815
51 UP5 0.472 0.822785
52 UML 0.467105 0.82716
53 Y6W 0.460177 0.88
54 4TC 0.453125 0.802469
55 U U 0.431034 0.888889
56 2QR 0.429577 0.817073
57 URI 0.425532 0.828571
58 U3P 0.415842 0.873239
59 UA3 0.415842 0.873239
60 PMP UD1 0.414966 0.804878
61 CSV 0.414634 0.893333
62 CSQ 0.414634 0.893333
63 CJB 0.412371 0.814286
64 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 : 5NDF; Ligand: UDP; Similar sites found with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 5ndf.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 4XFR CIT 1.17096
2 2V7B BEZ 1.51229
3 6EJ7 UDX 1.57618
4 1H5R THM 1.70648
5 3TTM PUT 1.7341
6 6FXR UDP 2.27671
7 5A07 GDP 2.30415
8 5VCM UDP 2.38663
9 5A1S FLC 2.45536
10 3ZF8 GDP 2.62295
11 2J0B UDP 2.85714
12 2VL8 CTS 2.9304
13 2VL8 UDP 2.9304
14 4K7O EKZ 2.97619
15 2WZG UPG 3.04762
16 1FHW I5P 3.10078
17 1O7Q UDP 3.11419
18 1O7Q GAL NAG 3.11419
19 1ZGS XMM 3.13199
20 3E3U NVC 3.5533
21 3CU0 UDP 3.55872
22 3CU0 GAL GAL SO4 3.55872
23 6CS8 F9Y 3.63036
24 1H7F C5P 3.67347
25 2NUN ADP 3.71517
26 2EB5 OXL 3.74532
27 3U2U UDP 3.80228
28 4GAH 0ET 3.82775
29 2W68 SIA GAL BGC 4.10256
30 3TW1 AHN 4.21941
31 3CKJ CIT 4.25532
32 5UQK U2F 4.30108
33 2GJP MAL 4.3299
34 4IRP UDP 4.78088
35 5W7B MYR 4.96454
36 1A99 PUT 5.23256
37 1PWB GLC GLC 5.64972
38 4MIX UD1 5.65476
39 2ZI8 SDT 5.66667
40 1LL2 UPG 5.70571
41 1WEI ADE 5.77778
42 6FFK D7Z 5.88235
43 2BVL UDP 5.89319
44 2BVL GLC 5.89319
45 2BO4 FLC 6.04534
46 2W9S TOP 6.21118
47 1XXA ARG 6.41026
48 2NU5 NAG 6.55738
49 2NUO BGC 6.55738
50 2HYQ MAN MAN 6.55738
51 1S4P GDP 6.6092
52 4M4K XYP XYP 6.62021
53 4M4K GDU 6.62021
54 5YSQ INS 6.64336
55 4RF7 ARG 6.83012
56 2AGD UDH 6.96864
57 2AGD NAG MAN BMA 6.96864
58 1YRO GDU 6.99301
59 2OVW CBI 7.05596
60 1MXG ACR 7.12644
61 1OMZ UD2 7.16724
62 4JD0 1KH 7.17131
63 2QGI UDP 7.25806
64 6M8N MLI 7.26392
65 1RL4 BL5 7.44681
66 2APC UDM 7.60234
67 1VBO MAN MAN MAN 8.05369
68 4DEC UDP 8.43023
69 4DEC 3PG 8.43023
70 5OES 3GC 9.31677
71 1LVW TYD 9.49153
72 1V84 UDP 11.8577
73 3V91 UPG 12.0275
74 2P6W FLC 12.6761
75 2UVO NDG 12.8655
76 2UVO NAG 12.8655
77 5MM0 GDD 13.1016
78 6A6A DAL 13.3333
79 5TZJ UD1 13.587
80 1QGQ UDP 14.902
81 1Q3P GLU ALA GLN THR ARG LEU 16.5138
82 6H21 UD1 18.8406
Pocket No.: 2; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: 84
This union binding pocket(no: 2) in the query (biounit: 5ndf.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 4XFR CIT 1.17096
2 6EJ7 UDX 1.57618
3 4PL9 ADP 1.63934
4 1H5S TMP 1.70648
5 1H5R THM 1.70648
6 1KC7 PPR 1.75131
7 6BSW UDP 1.77515
8 2VSS V55 1.81159
9 1OJJ GLC GAL 1.99005
10 3LTW HLZ 2.14286
11 6FXR UDP 2.27671
12 4DE3 DN8 2.28137
13 3GDN MXN 2.30326
14 5A07 GDP 2.30415
15 5VCM UDP 2.38663
16 5A1S FLC 2.45536
17 2J0B UDP 2.85714
18 6B9R 2HE 2.88889
19 2VL8 CTS 2.9304
20 2VL8 UDP 2.9304
21 4K7O EKZ 2.97619
22 3LKF PC 3.01003
23 1YFS ALA 3.01075
24 2WZG UPG 3.04762
25 1O7Q GAL NAG 3.11419
26 1O7Q UDP 3.11419
27 1ZGS XMM 3.13199
28 5KOD IAC 3.15236
29 1USF NAP 3.37079
30 3B6C SDN 3.4188
31 5OVK NDP 3.51562
32 3CU0 UDP 3.55872
33 3CU0 GAL GAL SO4 3.55872
34 6CS8 F9Y 3.63036
35 1H7F C5P 3.67347
36 3U2U UDP 3.80228
37 4GAH 0ET 3.82775
38 3CKJ CIT 4.25532
39 5UQK U2F 4.30108
40 3GD8 GOL 4.4843
41 4IRP UDP 4.78088
42 1DDU DDU 4.90566
43 5V4R MGT 4.93827
44 5W7B MYR 4.96454
45 3A76 SPD 5.11364
46 4MIX UD1 5.65476
47 1LL2 UPG 5.70571
48 6FFK D7Z 5.88235
49 2BVL GLC 5.89319
50 2BVL UDP 5.89319
51 2BO4 FLC 6.04534
52 2W9S TOP 6.21118
53 1XXA ARG 6.41026
54 2B6N ALA PRO THR 6.47482
55 2HYQ MAN MAN 6.55738
56 2NUO BGC 6.55738
57 2NU5 NAG 6.55738
58 2GUD MAN 6.55738
59 6CWH 6LA 6.59341
60 1S4P GDP 6.6092
61 4M4K GDU 6.62021
62 4M4K XYP XYP 6.62021
63 1YRO GDU 6.99301
64 1MXG ACR 7.12644
65 1OMZ UD2 7.16724
66 4JD0 1KH 7.17131
67 2QGI UDP 7.25806
68 2APC UDM 7.60234
69 4DEC 3PG 8.43023
70 4DEC UDP 8.43023
71 5ZJ5 GDP 8.64198
72 1J3I UMP 8.84146
73 3A16 PXO 8.84719
74 5OES 3GC 9.31677
75 1LVW TYD 9.49153
76 3KPE TM3 9.80392
77 1V84 UDP 11.8577
78 3V91 UPG 12.0275
79 5MM0 GDD 13.1016
80 3N29 GOL 13.3971
81 5TZJ UD1 13.587
82 1QGQ UDP 14.902
83 5H62 UDP 15.5172
84 6H21 UD1 18.8406
Pocket No.: 3; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 38
This union binding pocket(no: 3) in the query (biounit: 5ndf.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 4PL9 ADP 1.63934
2 1H5S TMP 1.70648
3 1KC7 PPR 1.75131
4 6BSW UDP 1.77515
5 2VSS V55 1.81159
6 5UC9 MYR 2.21239
7 3QPB URA 2.27671
8 4DE3 DN8 2.28137
9 5H3A UMP 2.4735
10 5AZC PGT 2.66667
11 5JCM ISD 2.88248
12 3LKF PC 3.01003
13 5KOD IAC 3.15236
14 3B6C SDN 3.4188
15 5AHO TLA 3.57143
16 4QM9 CYS 4.04624
17 6CB2 OLC 4.43686
18 3GD8 GOL 4.4843
19 6EV2 BGC 4.5045
20 1PIG BGC GLC 4.83871
21 5V4R MGT 4.93827
22 3A76 SPD 5.11364
23 5NDB 8TW 5.2
24 4XCP PLM 6.47059
25 2B6N ALA PRO THR 6.47482
26 4R3U 5AD 6.47986
27 2GUD MAN 6.55738
28 6CWH 6LA 6.59341
29 2Q4G CIT 6.97674
30 2R68 SUP 8.21643
31 3U40 ADN 8.26446
32 1J3I UMP 8.84146
33 3A16 PXO 8.84719
34 5DRB 5FJ 8.93471
35 4MPO AMP 9.15033
36 3KPE TM3 9.80392
37 3N29 GOL 13.3971
38 5H62 UDP 15.5172
Pocket No.: 4; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ndf.bio5) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 5ndf.bio5) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 3B6O TMP 3.64372
2 1HBK MYR 10.1124
3 2P6W FLC 12.6761
Pocket No.: 6; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 3
This union binding pocket(no: 6) in the query (biounit: 5ndf.bio5) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3LTW HLZ 2.14286
2 3B6O TMP 3.64372
3 1HBK MYR 10.1124
Pocket No.: 7; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 5
This union binding pocket(no: 7) in the query (biounit: 5ndf.bio3) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1UH4 GLC GLC GLC GLC GLC GLC 3.50263
2 5Z2L NDP 4.4898
3 6C8R SAH 4.74934
4 5KBF CMP 4.98339
5 5K8S CMP 10.1351
Pocket No.: 8; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 14
This union binding pocket(no: 8) in the query (biounit: 5ndf.bio3) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3QV9 QV7 1.40281
2 5EE7 5MV 1.54867
3 1W55 GPP 2.10158
4 1YXM ADE 2.64026
5 4RKX 3S9 2.68199
6 5OVK NDP 3.51562
7 2RDE C2E 4.38247
8 6CDZ UMP 4.94297
9 2WPF WPF 5.65657
10 2WPF FAD 5.65657
11 3AB4 THR 7.30337
12 5C2F JTH 10.0719
13 3FIU AMP 12.0482
14 2XKO AKG 12.3596
Pocket No.: 9; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: 14
This union binding pocket(no: 9) in the query (biounit: 5ndf.bio3) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 5EE7 5MV 1.54867
2 3TTM PUT 1.7341
3 5UC9 MYR 2.21239
4 1FHW I5P 3.10078
5 2NUN ADP 3.71517
6 6EV2 BGC 4.5045
7 1A99 PUT 5.23256
8 1Y7P RIP 6.27803
9 2AGD NAG MAN BMA 6.96864
10 2AGD UDH 6.96864
11 6M8N MLI 7.26392
12 3AB4 THR 7.30337
13 5C2F JTH 10.0719
14 3FIU AMP 12.0482
Pocket No.: 10; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: 18
This union binding pocket(no: 10) in the query (biounit: 5ndf.bio3) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 3QPB URA 2.27671
2 1UH4 GLC GLC GLC GLC GLC GLC 3.50263
3 3E3U NVC 3.5533
4 5AHO TLA 3.57143
5 1UJP CIT 3.69004
6 2GJP MAL 4.3299
7 6C8R SAH 4.74934
8 5NDB 8TW 5.2
9 1PWB GLC GLC 5.64972
10 4RF7 ARG 6.83012
11 2OVW CBI 7.05596
12 1VBO MAN MAN MAN 8.05369
13 3U40 ADN 8.26446
14 2GNK ATP 8.92857
15 1ONI BEZ 10.1449
16 2UVO NAG 12.8655
17 2UVO NDG 12.8655
18 6A6A DAL 13.3333
Pocket No.: 11; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 8
This union binding pocket(no: 11) in the query (biounit: 5ndf.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 5OKL PAM 1.75131
2 4XWT U5P 1.9678
3 3GDN MXN 2.30326
4 1TZD ADP 3.27273
5 4NRT 2NG 3.61217
6 6AYU MLI 4.03458
7 2GMP NAG MAN 6.74603
8 2Y6P CTP 11.9658
Pocket No.: 12; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: 3
This union binding pocket(no: 12) in the query (biounit: 5ndf.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1GA8 DEL 2.62697
2 5TCI MLI 2.68293
3 4WZ8 3W7 5.6042
Pocket No.: 13; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 5ndf.bio4) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 5ndf.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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