Receptor
PDB id Resolution Class Description Source Keywords
4OWK 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE VIBRIO VULNIFICUS HEMOLYSIN/CYTOLYS TREFOIL LECTIN WITH N-ACETYL-D-GALACTOSAMINE BOUND VIBRIO VULNIFICUS LECTIN PORE-FORMING TOXIN BETA-TREFOIL R-TYPE LECTIN TOX
Ref.: GLYCAN SPECIFICITY OF THE VIBRIO VULNIFICUS HEMOLYS OUTLINES EVOLUTIONARY HISTORY OF MEMBRANE TARGETING TOXIN FAMILY. J.MOL.BIOL. V. 426 2800 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NGA C:501;
A:501;
B:501;
G:501;
D:501;
E:501;
F:501;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
Kd = 131 uM
221.208 C8 H15 N O6 CC(=O...
GOL F:502;
A:502;
C:502;
G:502;
D:502;
E:502;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OWK 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE VIBRIO VULNIFICUS HEMOLYSIN/CYTOLYS TREFOIL LECTIN WITH N-ACETYL-D-GALACTOSAMINE BOUND VIBRIO VULNIFICUS LECTIN PORE-FORMING TOXIN BETA-TREFOIL R-TYPE LECTIN TOX
Ref.: GLYCAN SPECIFICITY OF THE VIBRIO VULNIFICUS HEMOLYS OUTLINES EVOLUTIONARY HISTORY OF MEMBRANE TARGETING TOXIN FAMILY. J.MOL.BIOL. V. 426 2800 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4OWK Kd = 131 uM NGA C8 H15 N O6 CC(=O)N[C@....
2 4OWL Kd = 152 uM GAL NAG n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4OWK Kd = 131 uM NGA C8 H15 N O6 CC(=O)N[C@....
2 4OWL Kd = 152 uM GAL NAG n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4OWK Kd = 131 uM NGA C8 H15 N O6 CC(=O)N[C@....
2 4OWL Kd = 152 uM GAL NAG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NGA; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG 1 1
2 HSQ 1 1
3 NGA 1 1
4 A2G 1 1
5 NDG 1 1
6 BM3 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 GAL NGA A2G 0.614035 0.816327
11 STZ 0.612245 0.65
12 16G 0.591837 0.735849
13 BMX 0.591837 0.735849
14 4QY 0.591837 0.735849
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NAG GDL 0.54386 0.833333
18 CBS 0.54386 0.833333
19 CBS CBS 0.54386 0.833333
20 NAG NDG 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 2F8 0.530612 0.909091
24 MAG 0.530612 0.909091
25 NLC 0.517857 0.888889
26 GAL NDG 0.517857 0.888889
27 NDG GAL 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 MAN NAG 0.508772 0.888889
32 4UZ 0.508475 0.808511
33 NDG NAG NAG 0.508197 0.816327
34 CTO 0.508197 0.816327
35 NAG NAG NDG 0.508197 0.816327
36 NAG NAG NAG NDG 0.508197 0.816327
37 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
38 NDG NAG NAG NDG 0.508197 0.816327
39 NAG NAG NAG NAG 0.508197 0.816327
40 NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NDG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 NDG NAG NAG NDG NAG 0.508197 0.816327
44 NDG NAG NAG NAG 0.508197 0.816327
45 NAG NAG NAG NAG NDG 0.508197 0.816327
46 NAG NAG NAG NAG NAG 0.508197 0.816327
47 NBG 0.5 0.951219
48 MQG 0.5 0.698113
49 A2G GAL 0.491228 0.888889
50 GAL A2G 0.491228 0.888889
51 GAL NGA 0.491228 0.888889
52 AMU 0.490909 0.930233
53 GN1 0.490566 0.754717
54 NG1 0.490566 0.754717
55 NDG NAG 0.47541 0.816327
56 NAG GAL 0.474576 0.888889
57 NGA GAL 0.474576 0.888889
58 NAG FUC 0.474576 0.866667
59 GAL NAG 0.474576 0.888889
60 NAG GAL NAG 0.455882 0.833333
61 FUC NAG 0.45 0.888889
62 3YW 0.448276 0.930233
63 GLA GAL NAG 0.446154 0.888889
64 MAN BMA NAG 0.446154 0.888889
65 NAG GAL GAL 0.446154 0.888889
66 FUL GAL NAG 0.426471 0.869565
67 G6S NAG 0.426471 0.677966
68 DR2 0.426471 0.869565
69 FUC GAL NDG 0.426471 0.869565
70 FUC GAL NAG 0.426471 0.869565
71 NDG GAL FUC 0.426471 0.869565
72 GYU 0.42623 0.740741
73 TNR 0.42623 0.833333
74 NAG BDP 0.421875 0.851064
75 NAG MBG 0.419355 0.851064
76 NGA GAL BGC 0.41791 0.888889
77 NAG NAG 0.415385 0.784314
78 AZC 0.415094 0.795918
79 SN5 SN5 0.412698 0.705882
80 MBG A2G 0.412698 0.851064
81 A2G MBG 0.412698 0.851064
82 HS2 0.411765 0.8125
83 5AX 0.411765 0.866667
84 6ZC 0.409091 0.655738
85 LEC 0.409091 0.655738
86 GAL BGC NAG GAL 0.408451 0.888889
87 TCG 0.408451 0.689655
88 CTO TMX 0.408451 0.689655
89 NAG NAG NAG NAG NAG NAG NAG 0.407895 0.740741
90 BMA 0.404762 0.7
91 WOO 0.404762 0.7
92 ALL 0.404762 0.7
93 GLA 0.404762 0.7
94 MAN 0.404762 0.7
95 GAL 0.404762 0.7
96 GLC 0.404762 0.7
97 GXL 0.404762 0.7
98 GIV 0.404762 0.7
99 BGC 0.404762 0.7
100 NAG AMU 0.402778 0.8
101 NAG MUB 0.402778 0.8
102 A2G GAL FUC 0.4 0.869565
103 DR3 0.4 0.869565
104 NAG GAL FUC 0.4 0.869565
105 FUC GL0 A2G 0.4 0.869565
106 A2G GLA FUC 0.4 0.869565
107 FUC GAL A2G 0.4 0.869565
108 NGA GAL FUC 0.4 0.869565
109 FUC GLA A2G 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 96
This union binding pocket(no: 1) in the query (biounit: 4owk.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LTN FMN 0.001069 0.46575 None
2 4LTN NAI 0.001241 0.46575 None
3 3FUR Z12 0.01097 0.45416 None
4 1EYR CDP 0.003547 0.45366 None
5 2Z9C FMN 0.003964 0.44259 None
6 4GAH 0ET 0.008547 0.43894 None
7 2FCR FMN 0.00658 0.43128 None
8 1AG9 FMN 0.00727 0.43066 None
9 1W4R TTP 0.01521 0.42311 None
10 2D0N PRO SER ILE ASP ARG SER THR LYS PRO 0.005734 0.41559 None
11 2CYE COA 0.0214 0.41185 None
12 3N5O GSH 0.01698 0.40991 None
13 2JAR UMP 0.02124 0.4097 None
14 2ORV 4TA 0.01946 0.40947 None
15 1FW1 GSH 0.01455 0.40805 None
16 5FBN 5WF 0.01756 0.40694 None
17 1EXF GLY 0.004074 0.40573 None
18 1VJE MSE 0.005423 0.42076 1.44928
19 4L6C 0BT 0.02547 0.41035 1.44928
20 2DWU DGL 0.01039 0.40389 1.44928
21 3GFS FMN 0.01057 0.4035 1.44928
22 1H7F C5P 0.0004345 0.49189 2.17391
23 1CZR FMN 0.004617 0.4472 2.17391
24 2X61 CH 0.02094 0.40029 2.17391
25 5MUA GAL 0.0000006529 0.48248 2.7972
26 2V1O COA 0.00802 0.44334 2.89855
27 4ZOM 4Q3 0.0375 0.42675 2.89855
28 3EJR HN4 0.01797 0.42672 2.89855
29 4N82 FMN 0.003108 0.42331 2.89855
30 3PLS ANP 0.03354 0.40053 2.89855
31 1HV9 UD1 0.01495 0.41226 3.62319
32 1GR0 NAD 0.04768 0.40358 3.62319
33 3RL3 5GP 0.01861 0.40191 3.62319
34 5UQW GDP 0.02058 0.41391 3.7037
35 3NBC LAT 0.0000007586 0.62441 4.34783
36 4PTZ FMN 0.004166 0.42327 4.34783
37 4XVX P6G FDA 0.01434 0.42253 4.34783
38 1KEW TYD 0.04053 0.41469 4.34783
39 2JFQ DGL 0.009968 0.40755 4.34783
40 1PN9 GTX 0.02037 0.40707 4.34783
41 1RE0 AFB 0.01051 0.40653 4.34783
42 5KOR GAL XYS XYS BGC BGC BGC XYS GAL BGC 0.01239 0.40612 4.34783
43 2DJH 3PD UM3 0.01366 0.40464 4.34783
44 4C2C ALA ALA ALA 0.013 0.40092 4.34783
45 2HIM ASN 0.01083 0.40004 4.34783
46 1J6X MET 0.008418 0.41427 5
47 4C0X FMN 0.005693 0.4478 5.07246
48 4C0X AQN 0.006965 0.4478 5.07246
49 4H2D FMN 0.008983 0.43847 5.07246
50 2XG9 NOJ GLC 0.02839 0.41989 5.07246
51 2P2V CSF 0.02614 0.40022 5.07246
52 3OIG NAD 0.0121 0.44481 5.7971
53 4O9C COA 0.008058 0.42785 5.7971
54 1BYG STU 0.008731 0.41381 5.7971
55 4R8L ASP 0.01333 0.41261 5.7971
56 1ZH8 NAP 0.04767 0.40622 5.7971
57 3JQ3 ADP 0.001699 0.44709 6.52174
58 3BJK CIT 0.01456 0.43748 6.52174
59 1E5D FMN 0.01329 0.42658 6.52174
60 2BME GNP 0.01184 0.42462 6.52174
61 1OS1 ATP 0.04334 0.40812 6.52174
62 1OS1 PYR 0.0453 0.40812 6.52174
63 1CTU ZEB 0.02051 0.41795 7.24638
64 3VEH 0GA 0.01122 0.41053 7.24638
65 1AIQ UMP 0.008222 0.42081 7.97101
66 1NCE UMP 0.01127 0.41426 7.97101
67 2Q97 ATP 0.04601 0.41366 7.97101
68 1ZPR UMP 0.009871 0.41177 7.97101
69 2VQO TFG 0.01374 0.40717 7.97101
70 4ISK UMP 0.0144 0.40014 7.97101
71 3FJO FMN 0.00764 0.43032 8.69565
72 2X24 X24 0.00578 0.42851 9.42029
73 4BGB ADP 0.006159 0.41952 10.1449
74 1VRP ADP 0.005488 0.41792 10.1449
75 4N65 FMN 0.02466 0.40943 10.1449
76 2DFV NAD 0.02519 0.40843 10.1449
77 4N65 AQN 0.0262 0.40538 10.1449
78 3OH3 UAD 0.01022 0.42743 12.3188
79 2Z48 A2G 0.00000186 0.57149 13.7681
80 2Z48 NGA 0.000008088 0.54012 13.7681
81 2Z49 AMG 0.0000154 0.49331 13.7681
82 3N39 FMN 0.005695 0.42743 13.7681
83 1JWY GDP 0.01189 0.4083 15.2174
84 1UWK URO 0.04951 0.4026 15.2174
85 1UWK NAD 0.04951 0.4026 15.2174
86 4BMO FMN 0.009601 0.40283 15.9664
87 4ZGR NGA GAL 0.0000000702 0.57453 16.6667
88 5F90 GLA GAL 0.008695 0.40575 17.3913
89 5F90 GLA GAL BGC 5VQ 0.01396 0.40046 17.3913
90 2ZQO NGA 0.0000001123 0.6803 18.4615
91 4K3P ACE GLN LEU ALA LEU PHE 0.01025 0.4306 18.8406
92 1ZEI CRS 0.003553 0.44727 18.8679
93 2D24 XYS XYS 0.000000186 0.61475 28.2609
94 5D63 FUC GLA GLA 0.00001758 0.57063 36.2319
95 5D63 FUC GAL GLA 0.00007305 0.5649 36.2319
96 1KNM LAT 0.00000001298 0.72763 38.4615
Pocket No.: 2; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 4owk.bio7) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GQR ADP 0.01506 0.40356 None
2 5C1P ADP 0.04558 0.40329 1.44928
3 3DDC GNP 0.04225 0.40294 3.61446
4 5DV2 C5P 0.01172 0.41383 3.62319
5 5GXU FMN 0.008414 0.41407 4.34783
6 3KA2 2NC 0.0435 0.4064 5.07246
7 4GLW NMN 0.006562 0.40541 5.07246
8 3HIW C2X 0.02126 0.41065 5.7971
9 4EIL UMP 0.008774 0.40393 5.7971
10 2AAZ UMP 0.01037 0.40177 5.7971
11 1NVU GTP 0.03934 0.40687 6.52174
12 3ZNR NU9 0.02028 0.40123 6.52174
13 5BZ4 COA 0.01683 0.40053 7.24638
14 1TSD UMP 0.002177 0.44729 7.97101
15 1TLC DGP 0.003137 0.44308 7.97101
16 1AXW UMP 0.00404 0.43217 7.97101
17 1F28 UMP 0.005241 0.42841 7.97101
18 2A9W UMP 0.005845 0.40115 7.97101
Pocket No.: 3; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 19
This union binding pocket(no: 3) in the query (biounit: 4owk.bio4) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JSR 1NQ 0.04047 0.43324 None
2 2Y9G LAT 0.009094 0.40308 None
3 2Y9G LBT 0.009094 0.40308 None
4 2GQS ADP 0.02342 0.402 None
5 1X1R GDP 0.04681 0.40626 2.17391
6 2OHH FMN 0.004528 0.45351 3.62319
7 4JIQ FMN 0.03164 0.41538 3.62319
8 4JIQ 1L5 0.03164 0.41538 3.62319
9 2ZYK GLC GLC GLC GLC GLC GLC GLC GLC 0.0267 0.40239 5.07246
10 1MJH ATP 0.02375 0.40034 5.07246
11 2VAP GDP 0.02502 0.40152 6.52174
12 1TLL FMN 0.01437 0.40931 7.24638
13 2BW7 APC 0.03369 0.40744 7.24638
14 1C7S CBS 0.02583 0.40133 7.97101
15 3RZ3 U94 0.01946 0.40333 9.42029
16 5H5J FAD 0.03906 0.40079 11.5942
17 5X8G S0N 0.04 0.40272 12.3188
18 4G6I RS3 0.03582 0.41103 13.7681
19 5NUL FMN 0.009117 0.42747 14.4928
Pocket No.: 4; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 9
This union binding pocket(no: 11) in the query (biounit: 4owk.bio6) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1R6D DAU 0.02599 0.4378 2.17391
2 1EK6 UPG 0.04746 0.41806 3.62319
3 1RHC F42 ACN 0.03695 0.41471 5.07246
4 4ONC 40B 0.04989 0.40261 5.07246
5 1M26 GAL A2G 0.005807 0.41727 5.26316
6 1V97 MTE 0.03835 0.42465 7.24638
7 1SYN UMP 0.003328 0.43849 7.97101
8 1UZN NAP 0.03354 0.40736 20.2899
9 4HDO GNP 0.03612 0.41003 24.6377
Pocket No.: 12; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 15
This union binding pocket(no: 12) in the query (biounit: 4owk.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1T5B FMN 0.002108 0.4662 None
2 1KHZ ADV 0.0128 0.42708 2.17391
3 1GRO ICT 0.0203 0.43905 3.62319
4 1D2N ANP 0.006734 0.41163 3.62319
5 1LLU NAD 0.01979 0.40744 4.34783
6 1SL4 MAN MAN MAN MAN 0.01311 0.40117 4.51613
7 2C91 NAP 0.02123 0.43653 5.07246
8 3EAU PDN 0.02356 0.43534 5.07246
9 4K81 GTP 0.03883 0.40236 5.26316
10 1AKV FMN 0.002937 0.44616 5.7971
11 1PZO CBT 0.04327 0.40574 5.7971
12 1NVV GNP 0.03032 0.41392 6.52174
13 5FUE UV4 0.0245 0.40546 6.52174
14 2A9K GDP 0.02529 0.40291 7.97101
15 3KUD GDP 0.02328 0.41335 19.7531
Pocket No.: 13; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 7
This union binding pocket(no: 13) in the query (biounit: 4owk.bio5) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IMI GSH 0.02159 0.40722 1.44928
2 1R18 SAH 0.04642 0.40822 4.34783
3 1W2T SUC GLA 0.01941 0.40095 6.52174
4 5M67 ADE 0.04941 0.42278 12.3188
5 4H2F ADN 0.02113 0.41174 13.0435
6 1V8B ADN 0.01939 0.40617 16.6667
7 3KJI ADP 0.04448 0.40153 17.3913
Pocket No.: 14; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found: 3
This union binding pocket(no: 14) in the query (biounit: 4owk.bio8) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1R6D NAD 0.03524 0.42764 2.17391
2 5T8U LPA 0.02538 0.4112 4.34783
3 3K87 FAD 0.04394 0.41064 7.24638
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