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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 1443 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 1205 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 1039 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: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA 1 1
2 NAG 1 1
3 A2G 1 1
4 BM3 1 1
5 HSQ 1 1
6 NDG 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 STZ 0.612245 0.65
11 4QY 0.591837 0.735849
12 BMX 0.591837 0.735849
13 16G 0.591837 0.735849
14 9C1 0.58 0.886364
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NDG NAG 0.54386 0.833333
18 CBS 0.54386 0.833333
19 NAG GDL 0.54386 0.833333
20 CBS CBS 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 MAG 0.530612 0.909091
24 2F8 0.530612 0.909091
25 NDG GAL 0.517857 0.888889
26 NLC 0.517857 0.888889
27 GAL NDG 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 4UZ 0.508475 0.808511
32 NAG NAG NAG NAG NDG 0.508197 0.816327
33 NDG NAG NAG NAG 0.508197 0.816327
34 NAG NAG NDG 0.508197 0.816327
35 NAG NAG NDG NAG 0.508197 0.816327
36 CTO 0.508197 0.816327
37 NDG NAG NAG NDG 0.508197 0.816327
38 NAG NAG NAG NDG 0.508197 0.816327
39 NDG NAG NAG 0.508197 0.816327
40 NAG NAG NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 MQG 0.5 0.698113
44 NBG 0.5 0.951219
45 GAL NGA 0.491228 0.888889
46 A2G GAL 0.491228 0.888889
47 GAL A2G 0.491228 0.888889
48 AMU 0.490909 0.930233
49 NG1 0.490566 0.754717
50 GN1 0.490566 0.754717
51 NAG GAL 0.474576 0.888889
52 GAL NAG 0.474576 0.888889
53 NAG FUC 0.474576 0.866667
54 NAG GAL NAG 0.455882 0.833333
55 3YW 0.448276 0.930233
56 GLA GAL NAG 0.446154 0.888889
57 MAN BMA NAG 0.446154 0.888889
58 NGA GAL 0.428571 0.869565
59 FUC GAL NAG 0.426471 0.869565
60 GAL NAG FUC 0.426471 0.869565
61 DR2 0.426471 0.869565
62 NAG GAL FUC 0.426471 0.869565
63 NDG GAL FUC 0.426471 0.869565
64 FUC GAL NDG 0.426471 0.869565
65 FUL GAL NAG 0.426471 0.869565
66 G6S NAG 0.426471 0.645161
67 TNR 0.42623 0.833333
68 GYU 0.42623 0.740741
69 GAL NGA A2G 0.424242 0.833333
70 NAG BDP 0.421875 0.851064
71 NAG MBG 0.419355 0.851064
72 NGA GAL BGC 0.41791 0.888889
73 NAG NDG 0.415385 0.784314
74 NAG NAG 0.415385 0.784314
75 AZC 0.415094 0.795918
76 SN5 SN5 0.412698 0.705882
77 A2G MBG 0.412698 0.851064
78 MBG A2G 0.412698 0.851064
79 HS2 0.411765 0.8125
80 5AX 0.411765 0.866667
81 NAG MAN BMA 0.411765 0.888889
82 6ZC 0.409091 0.655738
83 LEC 0.409091 0.655738
84 TCG 0.408451 0.689655
85 GAL BGC NAG GAL 0.408451 0.888889
86 NAG MAN 0.40625 0.851064
87 WOO 0.404762 0.7
88 MAN 0.404762 0.7
89 GAL 0.404762 0.7
90 BGC 0.404762 0.7
91 BMA 0.404762 0.7
92 GLA 0.404762 0.7
93 ALL 0.404762 0.7
94 GLC 0.404762 0.7
95 GXL 0.404762 0.7
96 GIV 0.404762 0.7
97 NAG AMU 0.402778 0.8
98 NAG MUB 0.402778 0.8
99 NAG A2G GAL 0.402778 0.833333
100 A2G GAL FUC 0.4 0.869565
101 FUC GLA A2G 0.4 0.869565
102 DR3 0.4 0.869565
103 A2G GLA FUC 0.4 0.869565
104 NGA GAL FUC 0.4 0.869565
105 FUC GAL 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 with APoc: 156
This union binding pocket(no: 1) in the query (biounit: 4owk.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4LTN NAI None
2 4LTN FMN None
3 2P4Y C03 None
4 3FUR Z12 None
5 1T5B FMN None
6 1EYR CDP None
7 2Z9C FMN None
8 2Z9C DTC None
9 4GAH 0ET None
10 2FCR FMN None
11 1AG9 FMN None
12 1W4R TTP None
13 2D0N PRO SER ILE ASP ARG SER THR LYS PRO None
14 3N5O GSH None
15 2ORV 4TA None
16 1FW1 GSH None
17 2CYE COA None
18 5FBN 5WF None
19 1WUR 8DG None
20 1EXF GLY None
21 1TLG GAL None
22 4WP9 ZDA None
23 1VJE MSE 1.44928
24 4L6C 0BT 1.44928
25 2DWU DGL 1.44928
26 3GFS FMN 1.44928
27 1H7F C5P 2.17391
28 1CZR FMN 2.17391
29 2DXU BT5 2.17391
30 2X61 CH 2.17391
31 5MUA GAL 2.7972
32 2V1O COA 2.89855
33 3EJR HN4 2.89855
34 4N82 FMN 2.89855
35 5NI5 8YB 2.89855
36 6AZQ C5J 2.89855
37 3PLS ANP 2.89855
38 2OHH FMN 3.62319
39 2QV6 GTP 3.62319
40 1HV9 UD1 3.62319
41 1GR0 NAD 3.62319
42 3RL3 5GP 3.62319
43 5ZCT ANP 3.62319
44 3NJ4 AFX 3.62319
45 5UQW GDP 3.7037
46 3NBC LAT 4.34783
47 4PTZ FMN 4.34783
48 4XVX P6G FDA 4.34783
49 3UG4 AHR 4.34783
50 5AK0 8V1 4.34783
51 1KEW TYD 4.34783
52 1PN9 GTX 4.34783
53 6EZ6 C5Z 4.34783
54 2JFQ DGL 4.34783
55 2PD4 DCN 4.34783
56 1RE0 AFB 4.34783
57 5KOR GAL XYS XYS BGC BGC BGC XYS GAL BGC 4.34783
58 2DJH 3PD UM3 4.34783
59 4XTX 590 4.34783
60 4C2C ALA ALA ALA 4.34783
61 2HIM ASN 4.34783
62 1J6X MET 5
63 4C0X AQN 5.07246
64 4C0X FMN 5.07246
65 4H2D FMN 5.07246
66 5N9T 8QQ 5.07246
67 2XG9 NOJ GLC 5.07246
68 5JH2 A2P 5.07246
69 5LMC FMN 5.07246
70 2GZM DGL 5.07246
71 1ZUW DGL 5.07246
72 2JLD AG1 5.07246
73 3OIG NAD 5.7971
74 1B1C FMN 5.7971
75 4O9C COA 5.7971
76 1BYG STU 5.7971
77 4R8L ASP 5.7971
78 1ZH8 NAP 5.7971
79 4O6W ACE PRO LEU 2SO SER TPO NH2 5.7971
80 3JQ3 ADP 6.52174
81 3BJK CIT 6.52174
82 3OJF NDP 6.52174
83 1E5D FMN 6.52174
84 2BME GNP 6.52174
85 6D5V GNP 6.52174
86 1OS1 ATP 6.52174
87 1OS1 PYR 6.52174
88 6D5H GNP 6.52174
89 6D55 GNP 6.52174
90 6GXA TB8 6.52174
91 6D5J GNP 6.52174
92 6D5E GNP 6.52174
93 6D56 GNP 6.52174
94 6D59 GNP 6.52174
95 6BVM GNP 6.52174
96 5F2T PLM 6.52174
97 2BW7 ECS 7.24638
98 1CTU ZEB 7.24638
99 3VEH 0GA 7.24638
100 2WSI FAD 7.24638
101 4TQK NAG 7.24638
102 1TLL FMN 7.24638
103 1AIQ UMP 7.97101
104 1F28 UMP 7.97101
105 1SYN UMP 7.97101
106 1NCE UMP 7.97101
107 1ZPR UMP 7.97101
108 6CDZ UMC 7.97101
109 6FYZ EBE 7.97101
110 2VVL FAD 7.97101
111 4ISK UMP 7.97101
112 1EFV FAD 8.69565
113 1EFV AMP 8.69565
114 3FJO FMN 8.69565
115 6HSJ COA 8.69565
116 1T36 ADP 8.69565
117 1UMG 2FP 8.69565
118 2X24 X24 9.42029
119 1CS4 101 10.1449
120 1CS4 FOK 10.1449
121 3HQ9 OXL 10.1449
122 4BGB ADP 10.1449
123 1VRP ADP 10.1449
124 4N65 FMN 10.1449
125 2DFV NAD 10.1449
126 4N65 AQN 10.1449
127 3ITJ FAD 10.1449
128 1O7Q UDP 10.8696
129 3OH3 UAD 12.3188
130 4DQL FAD 12.3188
131 2Z48 A2G 13.7681
132 2Z48 NGA 13.7681
133 2Z49 AMG 13.7681
134 3N39 FMN 13.7681
135 3LU1 NAD 13.7681
136 1YRO GDU 13.8211
137 5HZ9 5M8 14.0741
138 6F3M ADN 14.4928
139 1UWK NAD 15.2174
140 1UWK URO 15.2174
141 6AM8 PLT 15.942
142 4BMO FMN 15.9664
143 4ZGR NGA GAL 16.6667
144 4UXH T5A 16.6667
145 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 17
146 5F90 GLA GAL 17.3913
147 5F90 GLA GAL BGC 5VQ 17.3913
148 1QG6 TCL 18.1159
149 2ZQO NGA 18.4615
150 1ZEI CRS 18.8679
151 3MEH THP 22.4638
152 3A23 GAL 23.913
153 2D24 XYS XYS 28.2609
154 5D63 FUC GLA GLA 36.2319
155 5D63 FUC GAL GLA 36.2319
156 1KNM LAT 38.4615
Pocket No.: 2; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 53
This union binding pocket(no: 2) in the query (biounit: 4owk.bio7) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 2GQR ADP None
2 2GQS ADP None
3 5C1P ADP 1.44928
4 1WPY BTN 2.17391
5 1R6D DAU 2.17391
6 1R6D NAD 2.17391
7 5M06 ADP 2.17391
8 4BFW ZVW 2.17391
9 1X1R GDP 2.17391
10 6A9F 9BF 2.89855
11 4KBY C2E 2.89855
12 3DDC GNP 3.61446
13 1EK6 NAI 3.62319
14 1EK6 UPG 3.62319
15 5DV2 C5P 3.62319
16 5GXU FMN 4.34783
17 2VHL GLP 4.34783
18 4ONC 40B 5.07246
19 1RHC F42 ACN 5.07246
20 2R40 20E 5.07246
21 4GLW NMN 5.07246
22 2P2V CSF 5.07246
23 3TCT 3MI 5.51181
24 4AG5 ADP 5.7971
25 1PZO CBT 5.7971
26 3HIW C2X 5.7971
27 4EIL UMP 5.7971
28 2AAZ UMP 5.7971
29 6D5G GNP 6.52174
30 3NRR D16 6.52174
31 3NRR UMP 6.52174
32 6D5M GNP 6.52174
33 6D5L GNP 6.52174
34 1EP2 FMN 6.52174
35 3ZNR NU9 6.52174
36 1V97 MTE 7.24638
37 2BW7 APC 7.24638
38 5BZ4 COA 7.24638
39 1TSD UMP 7.97101
40 1TLC DGP 7.97101
41 1AXW UMP 7.97101
42 1JG0 UMP 7.97101
43 2A9W UMP 7.97101
44 4GLL NAD 8.69565
45 6HSP COA 8.69565
46 4UMX NAP 9.42029
47 4UMX VVS 9.42029
48 1BXK NAD 10.8696
49 4DPL NAP 11.5942
50 2WKV COA 12.3188
51 5OVL NAP 19.5652
52 5OVK NDP 19.5652
53 1UZN NAP 20.2899
Pocket No.: 3; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 23
This union binding pocket(no: 3) in the query (biounit: 4owk.bio4) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4JSR 1NQ None
2 2Y9G LBT None
3 2Y9G LAT None
4 2JAR UMP None
5 6ESN BWE 2.89855
6 4JIQ 1L5 3.62319
7 4JIQ FMN 3.62319
8 4XL4 COA 3.62319
9 1QK3 5GP 4.34783
10 2ZYK GLC GLC GLC GLC GLC GLC GLC GLC 5.07246
11 4HWS 1B3 5.07246
12 1MJH ATP 5.07246
13 2VAP GDP 6.52174
14 6ENO BJ8 7.24638
15 1C7S CBS 7.97101
16 2ART LPA AMP 8.69565
17 3RZ3 U94 9.42029
18 1O7Q GAL NAG 10.8696
19 5H5J FAD 11.5942
20 5X8G S0N 12.3188
21 4G6I RS3 13.7681
22 5NUL FMN 14.4928
23 4UBT COA 18.1159
Pocket No.: 4; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 8
This union binding pocket(no: 5) in the query (biounit: 4owk.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 5T8U LPA 4.34783
2 5AE9 OKO 4.34783
3 5OCG GNP 5.7971
4 3K87 FAD 7.24638
5 1U8Z GDP 7.24638
6 1W5F G2P 9.42029
7 4WZ8 3W7 13.7681
8 4HDO GNP 24.6377
Pocket No.: 6; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 24
This union binding pocket(no: 6) in the query (biounit: 4owk.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 5EQY 5RA None
2 4HEE 14R None
3 1S5P LYS GLY GLY ALA ALY ARG HIS ARG None
4 1KHZ ADV 2.17391
5 1GRO ICT 3.62319
6 1D2N ANP 3.62319
7 5LNQ CAA 3.62319
8 1LLU NAD 4.34783
9 1C7O PPG 4.34783
10 1SL4 MAN MAN MAN MAN 4.51613
11 2C91 NAP 5.07246
12 4PJT 2YQ 5.07246
13 4K81 GTP 5.26316
14 1AKV FMN 5.7971
15 6BVJ GNP 6.52174
16 6BVK GNP 6.52174
17 1NVV GNP 6.52174
18 6BVI GNP 6.52174
19 6BVL GNP 6.52174
20 2A9K GDP 7.97101
21 5M7S NHT 7.97101
22 2J62 GSZ 8.69565
23 2QFY AKG 9.42029
24 3KUD GDP 19.7531
Pocket No.: 7; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 18
This union binding pocket(no: 8) in the query (biounit: 4owk.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5EYG NAP None
2 2IMI GSH 1.44928
3 1A8R GTP 2.17391
4 5UIJ TYD 2.89855
5 2ZEJ GDP 4.34783
6 6CI9 NAP 5.07246
7 5O1I 9GH 5.07246
8 5ND5 TPP 5.7971
9 2ZJ1 ARJ 6.52174
10 2ZJ1 NAD 6.52174
11 1W2T SUC GLA 6.52174
12 5ECS GSH 8.69565
13 5M67 NAD 12.3188
14 5M67 ADE 12.3188
15 4H2F ADN 13.0435
16 6AMI TRP 15.942
17 1V8B ADN 16.6667
18 6DIO NAD 18.8406
Pocket No.: 9; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: 7
This union binding pocket(no: 10) in the query (biounit: 4owk.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 1RLZ NAD 2.89855
2 1PZM 5GP 5.07246
3 1M26 GAL A2G 5.26316
4 2Q1W NAD 6.52174
5 4L77 CNL 7.24638
6 5U6C 7YS 7.24638
7 3DGB MUC 8.69565
Pocket No.: 11; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 4owk.bio6) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 4OWK; Ligand: NGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 4owk.bio3) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio5) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 4OWK; Ligand: NGA; 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: 4owk.bio8) has 8 residues
No: Leader PDB Ligand Sequence Similarity
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