Receptor
PDB id Resolution Class Description Source Keywords
2BVE 2.2 Å NON-ENZYME: IMMUNE STRUCTURE OF THE N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH 2-PHENYL-PROP5AC MUS MUSCULUS IMMUNE SYSTEM IMMUNOGLOBULIN LECTIN SUPERFAMILY CARBOHYDRATE BINDING SIGLEC INHIBITOR DESIGN CELL ADHESION
Ref.: CRYSTALLOGRAPHIC AND IN SILICO ANALYSIS OF THE SIALOSIDE-BINDING CHARACTERISTICS OF THE SIGLEC SIALOADHESIN. J.MOL.BIOL. V. 365 1469 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PH5 A:1120;
B:1119;
Valid;
Valid;
none;
none;
ic50 = 215 uM
413.419 C19 H27 N O9 CCC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2BVE 2.2 Å NON-ENZYME: IMMUNE STRUCTURE OF THE N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH 2-PHENYL-PROP5AC MUS MUSCULUS IMMUNE SYSTEM IMMUNOGLOBULIN LECTIN SUPERFAMILY CARBOHYDRATE BINDING SIGLEC INHIBITOR DESIGN CELL ADHESION
Ref.: CRYSTALLOGRAPHIC AND IN SILICO ANALYSIS OF THE SIALOSIDE-BINDING CHARACTERISTICS OF THE SIGLEC SIALOADHESIN. J.MOL.BIOL. V. 365 1469 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 1OD9 - BND C19 H26 N2 O9 CC(=O)N[C@....
2 2BVE ic50 = 215 uM PH5 C19 H27 N O9 CCC(=O)N[C....
3 1URL - ALA GLY HIS THR TRP GLY HIA SIA n/a n/a
4 1QFO - SIA C11 H19 N O9 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 1OD9 - BND C19 H26 N2 O9 CC(=O)N[C@....
2 2BVE ic50 = 215 uM PH5 C19 H27 N O9 CCC(=O)N[C....
3 1URL - ALA GLY HIS THR TRP GLY HIA SIA n/a n/a
4 1QFO - SIA C11 H19 N O9 CC(=O)N[C@....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 1OD9 - BND C19 H26 N2 O9 CC(=O)N[C@....
2 2BVE ic50 = 215 uM PH5 C19 H27 N O9 CCC(=O)N[C....
3 1URL - ALA GLY HIS THR TRP GLY HIA SIA n/a n/a
4 1QFO - SIA C11 H19 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PH5; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 PH5 1 1
2 MN0 0.53012 0.851852
3 18D 0.52439 0.865385
4 MNA 0.493976 0.818182
5 423 0.471698 0.662338
6 SIA CMO 0.453488 0.803571
7 BND 0.44898 0.807018
8 425 0.423423 0.662338
9 MUS 0.420561 0.766667
10 GAL SIA 0.42 0.872727
11 NGC 0.413793 0.846154
12 4U0 0.403509 0.888889
13 4U1 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BVE; Ligand: PH5; Similar sites found: 155
This union binding pocket(no: 1) in the query (biounit: 2bve.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OHU 2TK 0.0176 0.44397 None
2 4OHU NAD 0.0176 0.44397 None
3 3O7J 2AL 0.008962 0.42528 None
4 1JIF CU BLM 0.02285 0.42383 None
5 1CLU DBG 0.01557 0.42336 None
6 3E5H GNP 0.02008 0.41464 None
7 1HFS L04 0.04258 0.40718 None
8 1L6O SER LEU LYS LEU MET THR THR VAL 0.017 0.40265 None
9 2CYE COA 0.01698 0.40085 None
10 4TWP AXI 0.005413 0.47608 1.68067
11 5KJK 6T1 0.005277 0.46573 1.68067
12 5KJK SAM 0.005277 0.46573 1.68067
13 3PBB PBD 0.008874 0.43051 1.68067
14 4CS4 ANP 0.01717 0.42425 1.68067
15 4CS4 AXZ 0.02109 0.42425 1.68067
16 4IPH 1FJ 0.001797 0.47982 2.52101
17 3D78 NBB 0.01768 0.42 2.52101
18 5AX9 4KT 0.02076 0.41238 2.52101
19 1U7Z PMT 0.0171 0.40703 2.52101
20 3S2Y FMN 0.02042 0.40541 2.52101
21 4P5E N6P 0.02728 0.40392 2.52101
22 5E6O TRP GLU GLU LEU 0.001227 0.46836 2.54237
23 2VNF ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.008812 0.41903 3.33333
24 5TO8 7FM 0.01879 0.44564 3.36134
25 5CJ3 52G 0.01504 0.44285 3.36134
26 2G86 UMP 0.03649 0.42112 3.36134
27 3F7Z 34O 0.01495 0.40784 3.36134
28 1CT9 GLN 0.01383 0.40643 3.36134
29 4JIZ TYR HIS SEP VAL VAL ARG TYR ALA 0.003182 0.43507 4.20168
30 4EOY ASN ASP TRP LEU LEU PRO SER TYR 0.003668 0.43251 4.20168
31 5XDT MB3 0.01661 0.42849 4.20168
32 4I54 1C1 0.02041 0.42395 4.20168
33 4HIA FMN 0.02564 0.42112 4.20168
34 2Y4O DLL 0.02612 0.40961 4.20168
35 2P3I MNA 0.004859 0.40323 4.20168
36 5FA8 SAM 0.03122 0.40118 4.20168
37 4AGQ P96 0.03875 0.40003 4.20168
38 5L83 ASP TRP GLU ILE VAL 0.003655 0.43039 4.46429
39 4YEF 4CQ 0.01063 0.43348 4.49438
40 2P4T NAP 0.01173 0.40822 4.83871
41 2BSA FAD 0.002954 0.49353 5.04202
42 2BSA NAP 0.003047 0.49353 5.04202
43 5LXI GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 0.002041 0.46327 5.04202
44 2AMV BIN 0.02095 0.41978 5.04202
45 4Z5W TYS ILE TYS THR GLN 0.01582 0.41485 5.04202
46 4FJU GLV 0.04904 0.40271 5.04202
47 4FJU NAI 0.04702 0.40271 5.04202
48 5W4W 9WG 0.04513 0.40209 5.04202
49 2I0D MUT 0.01725 0.45961 5.05051
50 1XNK XS2 0.01748 0.40811 5.10204
51 1GMN IDS SGN IDS SGN IDS 0.001453 0.45634 5.88235
52 5CCM 4ZX 0.01374 0.44147 5.88235
53 5CCM SAM 0.01205 0.44073 5.88235
54 3AQV TAK 0.006465 0.43094 5.88235
55 1YB5 NAP 0.01293 0.42767 5.88235
56 4OXI GAP 0.01227 0.42483 5.88235
57 5TA6 79D 0.03422 0.41129 5.88235
58 5UR1 YY9 0.03821 0.41111 5.88235
59 3KRU FMN 0.04427 0.41034 5.88235
60 3FW3 GLC 0.007723 0.40839 5.88235
61 1ZC3 GNP 0.04294 0.40808 5.88235
62 4KVG GTP 0.02438 0.40652 5.88235
63 3RY8 FLC 0.01322 0.40605 5.88235
64 5VW2 NAP 0.006791 0.4658 6.72269
65 5VW2 FDA 0.006791 0.4658 6.72269
66 5EOB 5QQ 0.03701 0.43468 6.72269
67 4B0H DUR 0.04474 0.41672 6.72269
68 1NME 159 0.001907 0.41619 6.72269
69 3E7O 35F 0.0423 0.41461 6.72269
70 5U61 7WG 0.04573 0.41416 6.72269
71 3TTZ 07N 0.01564 0.40828 6.72269
72 3PTG 932 0.01582 0.408 6.72269
73 2C94 TSF 0.04037 0.40521 6.72269
74 1RY2 AMP 0.02259 0.40397 6.72269
75 5EYK 5U5 0.04909 0.40171 6.77966
76 3ZJ0 ACO 0.02735 0.41543 6.79612
77 4O6W ACE PRO LEU 2SO SER TPO NH2 0.002146 0.47126 7.56302
78 4BTK DTQ 0.002874 0.46625 7.56302
79 2RKV COA 0.0108 0.4378 7.56302
80 2RKV ZBA 0.01223 0.4378 7.56302
81 5IBP ACE ASP GLU VAL ASP 0QE 0.01858 0.43069 7.56302
82 4YZC STU 0.03919 0.42192 7.56302
83 3P3G 3P3 0.0234 0.4106 7.56302
84 3P3G UKW 0.0234 0.4106 7.56302
85 5BVE 4VG 0.04322 0.41033 7.56302
86 1II5 GLU 0.008998 0.40966 7.56302
87 1KQ4 FAD 0.04292 0.40462 7.56302
88 2F57 23D 0.02461 0.40248 7.56302
89 4II2 ATP 0.04085 0.40196 7.56302
90 2J3M PRI 0.004691 0.45914 8.40336
91 2J3M ATP 0.004326 0.45784 8.40336
92 1B7H LYS NLE LYS 0.003963 0.45357 8.40336
93 4RPL 3UC 0.02706 0.43898 8.40336
94 4RPL FAD 0.02774 0.43765 8.40336
95 4FAI PBD 0.005629 0.42167 8.40336
96 5JFT ACE ASP GLU VAL ASP 0QE 0.00698 0.4204 8.40336
97 2ED4 FAD 0.01631 0.41184 8.40336
98 2GU8 796 0.03231 0.40997 8.40336
99 4LO6 SIA GAL 0.0004976 0.40775 8.40336
100 3G35 F13 0.03088 0.40692 8.40336
101 2X06 NAD 0.03582 0.4061 8.40336
102 1MWH GTG 0.03102 0.40099 8.40336
103 5KIQ SIA GAL NAG FUC 0.003169 0.43655 9.2437
104 5FI4 5XV 0.01617 0.42875 9.2437
105 2X4Z X4Z 0.01866 0.42659 9.2437
106 5A89 FMN 0.03436 0.42323 9.2437
107 5A89 ADP 0.03224 0.42323 9.2437
108 1KQB FMN 0.02416 0.42014 9.2437
109 1KQB BEZ 0.02557 0.42014 9.2437
110 5DXT 5H5 0.03035 0.40877 9.2437
111 1SG4 CO8 0.02795 0.40638 9.2437
112 4GID 0GH 0.009825 0.47204 10.084
113 2RGO FAD 0.03709 0.40976 10.084
114 2V0C ANZ 0.01277 0.40594 10.084
115 5JZJ AN2 0.03222 0.40508 10.084
116 4G17 0VN 0.01681 0.41142 10.303
117 3DLG GWE 0.02559 0.43213 10.9244
118 4HWT 1B2 0.03116 0.40694 10.9244
119 4MNS 2AX 0.01606 0.44544 11.7647
120 1W7F ICT 0.007638 0.42782 11.7647
121 3M8U GDS 0.02649 0.41699 11.7647
122 2Y91 98J 0.009058 0.41093 11.7647
123 4YZN 4K5 0.03715 0.40634 12.605
124 5LIA 6XN 0.009504 0.45447 13.4454
125 4DS0 A2G GAL NAG FUC 0.001995 0.43194 13.4454
126 3E9I XAH 0.009645 0.42464 13.4454
127 3A5Z KAA 0.02417 0.4234 13.4454
128 3A5Y KAA 0.01096 0.41663 13.4454
129 5U3B 7TD 0.03797 0.40206 13.4454
130 3GD9 GLC BGC BGC BGC 0.03164 0.40156 13.4454
131 1BH2 GSP 0.03829 0.40113 13.4454
132 3NYQ AMP 0.02446 0.42321 14.2857
133 3NYQ MCA 0.02346 0.42321 14.2857
134 4EUU BX7 0.03804 0.40965 14.2857
135 1TAD GDP 0.03061 0.40624 14.2857
136 1TAD ALF 0.03061 0.40624 14.2857
137 3R5J ACE ALA ASP VAL ALA ASA 0.00977 0.41286 15
138 3BIY 01K 0.02017 0.42082 15.126
139 2RCU BUJ 0.03429 0.43516 15.9664
140 3TAY MN0 0.02637 0.41854 17.6471
141 5TUZ SAM 0.01336 0.43589 18.4874
142 5TUZ 7L6 0.01336 0.43589 18.4874
143 5L0U 660 0.03052 0.40234 18.4874
144 4ZTE 4RL 0.02547 0.40354 19.3277
145 3IES M24 0.01514 0.43694 20.1681
146 5ALC TIQ 0.03397 0.40229 21.8487
147 4PYW ACE THR THR ALA ILE NH2 0.01703 0.41654 22.6891
148 3WYJ H78 0.02694 0.43385 23.5294
149 5DQ8 FLF 0.01732 0.42935 23.5294
150 2WEL K88 0.01038 0.40966 23.5294
151 3G5D 1N1 0.04516 0.42239 26.0504
152 5T0B SIA GAL NAG 0.03102 0.40665 28.5714
153 4DVR 0LY 0.02108 0.40053 28.5714
154 2HRL SIA GAL SIA BGC NGA CEQ 0.00008231 0.52827 38.5827
155 5LFV SIA GAL NAG 0.0002487 0.47537 47.8992
Pocket No.: 2; Query (leader) PDB : 2BVE; Ligand: PH5; Similar sites found: 48
This union binding pocket(no: 2) in the query (biounit: 2bve.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AYF C7H 0.00813 0.41372 None
2 5AYF SAM 0.007458 0.41372 None
3 4O1M NAD 0.03305 0.41087 2.52101
4 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.002375 0.40922 3
5 4KQR VPP 0.00288 0.43379 3.36134
6 1W0H AMP 0.003579 0.40102 3.36134
7 4UMX NAP 0.04168 0.44115 4.20168
8 4UMX VVS 0.04242 0.44115 4.20168
9 1D01 ACE MET LEU SER VAL GLU GLU GLU GLY 0.02113 0.41633 4.20168
10 4DA6 GA2 0.007545 0.40679 4.20168
11 3E7W AMP 0.02234 0.42476 5.04202
12 1AMU AMP 0.02618 0.40661 5.04202
13 3U40 ADN 0.01131 0.40579 5.04202
14 5EW9 5VC 0.04229 0.41088 5.88235
15 5D9G GLU ASN LEU TYR PHE GLN 0.02189 0.40694 5.88235
16 5FA6 NAP 0.02205 0.42751 6.72269
17 5FA6 FAD 0.02166 0.42751 6.72269
18 5FA6 FMN 0.02166 0.42751 6.72269
19 5H5J FAD 0.0212 0.40584 6.72269
20 3KJD 78P 0.01456 0.40337 6.72269
21 4MOB ADP 0.02428 0.40447 7.56302
22 2EXX NAP 0.03347 0.40061 7.56302
23 4TSZ ACE GLN ALC ASP LEU ZCL 0.01493 0.42463 8.40336
24 3DHV DAL AMP 0.02411 0.42228 8.40336
25 1AFS NAP 0.03375 0.42167 8.40336
26 2EW5 Y12 0.01312 0.40974 8.40336
27 2WZ5 MET 0.009846 0.40479 8.40336
28 4QAR ADE 0.02114 0.40293 9.2437
29 5TVF CGQ 0.003112 0.46144 10.084
30 3SVL FMN 0.004885 0.44076 10.084
31 2WSA MYA 0.03443 0.42722 10.084
32 2WSA 646 0.03443 0.42722 10.084
33 5LRT ADP 0.02008 0.42374 10.084
34 1I1E DM2 0.009015 0.40715 10.084
35 2ICK DMA 0.04379 0.40166 10.084
36 4BMX ADE 0.004416 0.43864 11.7647
37 3TNF GNP 0.01325 0.41979 11.7647
38 4WKB TDI 0.02726 0.4128 12.605
39 2ODE ALF GDP 0.0465 0.40048 12.605
40 3LVW GSH 0.006604 0.44874 14.2857
41 5F1R 42O 0.02933 0.42566 14.2857
42 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.006627 0.42138 16.8067
43 5MSD AMP 0.006385 0.40656 18.4874
44 4D79 ATP 0.01091 0.40019 18.4874
45 2CKM AA7 0.0297 0.44596 21.0084
46 2R4J 13P 0.0429 0.40167 23.5294
47 2W5Z SAH 0.003806 0.40298 26.0504
48 4BH1 SIA GAL NAG 0.01043 0.42565 30.2521
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