Receptor
PDB id Resolution Class Description Source Keywords
3DUR 1.86 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF SAG173-04 MUS MUSCULUS ANTIBODY KDO TWINNING PSEUDO-SYMMETRY IMMUNE SYSTEM
Ref.: PSEUDO-SYMMETRY AND TWINNING IN CRYSTALS OF HOMOLOGOUS ANTIBODY FV FRAGMENTS. ACTA CRYSTALLOGR.,SECT.D V. 64 1250 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KDO A:303;
D:303;
Valid;
Valid;
none;
none;
submit data
238.192 C8 H14 O8 C1[C@...
MG A:107;
C:108;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
PG4 B:112;
D:304;
Invalid;
Invalid;
none;
none;
submit data
194.226 C8 H18 O5 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DUR 1.86 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF SAG173-04 MUS MUSCULUS ANTIBODY KDO TWINNING PSEUDO-SYMMETRY IMMUNE SYSTEM
Ref.: PSEUDO-SYMMETRY AND TWINNING IN CRYSTALS OF HOMOLOGOUS ANTIBODY FV FRAGMENTS. ACTA CRYSTALLOGR.,SECT.D V. 64 1250 2008
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 3DUS - KDO C8 H14 O8 C1[C@H]([C....
2 3DUR - KDO C8 H14 O8 C1[C@H]([C....
3 3DV4 - KDO C8 H14 O8 C1[C@H]([C....
4 3DUU - KDO C8 H14 O8 C1[C@H]([C....
5 3DV6 - KDO C8 H14 O8 C1[C@H]([C....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 2BFV - STG C24 H32 O9 C[C@]12CC[....
2 1BFV Ka ~ 10000000 M^-1 STG C24 H32 O9 C[C@]12CC[....
3 1CFV Ka ~ 100000000 M^-1 E3G C24 H30 O8 C[C@]12CC[....
4 2CJU - PHX C14 H14 N2 O4 c1ccc(cc1)....
5 1WZ1 - DNS C18 H25 N3 O4 S CN(C)c1ccc....
6 43CA Kd < 1 uM NPO C6 H5 N O3 c1cc(ccc1[....
7 3DUS - KDO C8 H14 O8 C1[C@H]([C....
8 3DUR - KDO C8 H14 O8 C1[C@H]([C....
9 3DV4 - KDO C8 H14 O8 C1[C@H]([C....
10 3DUU - KDO C8 H14 O8 C1[C@H]([C....
11 3DV6 - KDO C8 H14 O8 C1[C@H]([C....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 2BFV - STG C24 H32 O9 C[C@]12CC[....
2 1BFV Ka ~ 10000000 M^-1 STG C24 H32 O9 C[C@]12CC[....
3 1CFV Ka ~ 100000000 M^-1 E3G C24 H30 O8 C[C@]12CC[....
4 2CJU - PHX C14 H14 N2 O4 c1ccc(cc1)....
5 1WZ1 - DNS C18 H25 N3 O4 S CN(C)c1ccc....
6 43CA Kd < 1 uM NPO C6 H5 N O3 c1cc(ccc1[....
7 3DUS - KDO C8 H14 O8 C1[C@H]([C....
8 3DUR - KDO C8 H14 O8 C1[C@H]([C....
9 3DV6 - KDO C8 H14 O8 C1[C@H]([C....
10 1DL7 Kd = 0.32 uM NCH C11 H18 N2 O6 P C[N+](C)(C....
11 2E27 Ka = 2220000000 M^-1 AB0 C16 H24 O8 COCO[C@H]1....
12 1OAR Kd = 40 nM AZN C14 H8 O7 S c1ccc2c(c1....
13 2BJM Ka < 100000 M^-1 ANF C14 H10 O c1ccc2c(c1....
14 1A6V - NPC C14 H17 N2 O6 c1cc(c(cc1....
15 3T0X - DIW C26 H29 N2 O3 S CC1(c2cccc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KDO; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 KDO 1 1
2 KDN 0.64 0.96875
3 KDM 0.64 0.96875
4 KDE 0.467742 0.864865
5 SLB 0.435484 0.704545
6 SIA 0.435484 0.704545
7 KDF 0.428571 0.833333
8 KDO KDO KDO 0.422535 0.8
9 NGC 0.421875 0.688889
10 18D 0.409091 0.673913
11 42D 0.409091 0.645833
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DUR; Ligand: KDO; Similar sites found: 84
This union binding pocket(no: 1) in the query (biounit: 3dur.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2PN6 GLN 0.02872 0.42936 None
2 3ZZS TRP 0.0199 0.41352 None
3 1WKL ATP 0.03922 0.41226 None
4 1WKL ADP 0.04672 0.40168 None
5 1QJC PNS 0.006669 0.45061 1.65289
6 1SS4 CIT 0.01989 0.44634 2.47934
7 1OD6 PNS 0.001664 0.47836 2.67857
8 1O6B ADP 0.003128 0.45995 2.67857
9 1WVC CTP 0.01697 0.44601 2.67857
10 2C1Q BTN 0.03346 0.40684 4.13223
11 1FS5 TLA 0.01832 0.40638 4.13223
12 2R7K ACP 0.03351 0.43489 4.46429
13 2R7K AMZ 0.03351 0.43489 4.46429
14 1DR1 HBI 0.03632 0.40331 4.46429
15 1DR1 NAP 0.03632 0.40331 4.46429
16 4KCF FMN 0.01298 0.42419 4.95868
17 4C25 13P 0.01424 0.41326 4.95868
18 4A8T PAO 0.008817 0.45004 5.35714
19 4JP3 CIT 0.006553 0.43349 5.35714
20 1QW9 KHP 0.01369 0.40999 5.35714
21 2FMD MAN MAN 0.009147 0.4097 5.35714
22 1G6O ADP 0.01754 0.43139 5.78512
23 4P87 4NP 0.01283 0.41264 5.78512
24 1I2B UPG 0.03698 0.44044 6.25
25 1I2B NAD 0.03698 0.44044 6.25
26 1I2B USQ 0.03698 0.44044 6.25
27 1ZFJ IMP 0.0283 0.43911 6.25
28 1YOA FMN 0.01999 0.41352 6.25
29 4TMK T5A 0.02797 0.44369 6.61157
30 3IU9 T07 0.0332 0.41981 6.61157
31 2QXX TTP 0.01573 0.41825 6.61157
32 1V8K ANP 0.01723 0.41196 6.61157
33 1G7V PAI 0.02779 0.41065 6.61157
34 1V5F TPP 0.006587 0.48546 7.14286
35 1V5F FAD 0.006587 0.48546 7.14286
36 3Q2I HP7 0.04001 0.41763 7.14286
37 2ET1 GLV 0.03263 0.40644 7.14286
38 4QVH FLC 0.006612 0.46292 8.03571
39 3UC5 ATP 0.01635 0.43492 8.03571
40 4CMF PXG 0.02112 0.42459 8.26446
41 1XP8 AGS 0.02944 0.41376 8.26446
42 3ZV6 NAD 0.02939 0.41128 8.26446
43 3ZV6 4HB 0.03064 0.41128 8.26446
44 4AF0 MOA 0.01095 0.41284 8.92857
45 2JEN GLC GLC BGC XYS BGC XYS 0.01342 0.44646 9.09091
46 2JEN GLC GLC XYS XYS 0.01959 0.4222 9.09091
47 4U36 TNR 0.007407 0.42034 9.82143
48 1MVQ MMA 0.02501 0.40457 9.82143
49 1OFH ADP 0.01837 0.40429 9.82143
50 1JA9 NDP 0.02278 0.4333 9.91736
51 4QDF 30Q 0.002861 0.44244 10.7143
52 2RDT 2RD 0.03286 0.42422 10.7143
53 1Z4V DAN 0.003952 0.44352 10.7438
54 1VQ2 DDN 0.0197 0.43288 10.7438
55 3EJ0 11X 0.005985 0.42595 10.7438
56 1NME 159 0.00354 0.41911 10.8696
57 3TA2 AKG 0.02394 0.40305 11.0169
58 1RYI FAD 0.02245 0.41855 11.5702
59 1RYI GOA 0.02645 0.41516 11.5702
60 1LCP PLU 0.01601 0.40696 11.5702
61 3CKZ ZMR 0.04702 0.40155 11.5702
62 4MOB ADP 0.006108 0.4124 11.6071
63 3NJQ NJQ 0.01237 0.41336 13.2231
64 3UXL CFI 0.01848 0.446 13.3929
65 4UBP HAE 0.008467 0.41204 13.3929
66 1Q3Q ANP 0.01156 0.44159 14.0496
67 3MB5 SAM 0.04137 0.41042 14.0496
68 1WL4 COA 0.01347 0.42908 14.2857
69 1GSA GSH 0.02222 0.41704 14.2857
70 1NVU GTP 0.04321 0.41223 14.2857
71 2GGH NLQ 0.04258 0.40005 14.2857
72 3CH5 GDP 0.0218 0.40956 15.3846
73 3CXO 3LR 0.007176 0.42667 16.0714
74 1DXY NAD 0.03364 0.43354 16.5289
75 2VMD MBG 0.0002258 0.40383 16.5289
76 4Q3R XA2 0.02027 0.40239 16.9643
77 1HV9 UD1 0.005513 0.44832 17.8571
78 4DA6 GA2 0.04783 0.41005 17.8571
79 3CL7 HYN 0.01335 0.40902 17.8571
80 1A5Z NAD 0.02493 0.41959 18.75
81 2VHJ ADP 0.0147 0.40078 19.6429
82 1OMZ UD2 0.01694 0.42436 21.4286
83 1JOT GAL A2G 0.006573 0.40308 23.1405
84 1GR0 NAD 0.01424 0.44572 30.5785
Pocket No.: 2; Query (leader) PDB : 3DUR; Ligand: KDO; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 3dur.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DUA OXL 0.01013 0.40278 None
2 1SS4 GSH 0.02741 0.41448 2.47934
3 1KW6 BPY 0.02596 0.42254 4.46429
4 1V1A ADP 0.01152 0.41249 6.61157
5 4NVP 7CH 0.02966 0.40114 6.61157
6 2NLI LAC 0.03507 0.40969 7.14286
7 2NLI FMN 0.03507 0.40969 7.14286
8 4KS1 2H8 0.02668 0.41059 8.26446
9 2BJK NAD 0.03787 0.40987 8.26446
10 4AF0 IMP 0.04096 0.40505 8.92857
11 2ZI8 SDT 0.01213 0.41151 9.09091
12 2P8B NSK 0.02169 0.44379 9.91736
13 2RDT FMN 0.02595 0.41867 10.7143
14 2ZX7 ZX7 0.005563 0.42825 10.7438
15 3TA2 ATP 0.01871 0.40854 11.0169
16 4HPP GLU 0.01182 0.41908 11.5702
17 1X1T NAD 0.01512 0.43856 11.6071
18 1K97 CIR 0.0335 0.42576 11.6071
19 1K97 ASP 0.0335 0.42576 11.6071
20 3EAU PDN 0.02568 0.43049 12.5
21 3EAU NDP 0.02568 0.43049 12.5
22 3HPF GAE 0.02111 0.40779 13.2231
23 2J5S KTA 0.01033 0.4006 13.3929
24 3SUC ATP 0.03258 0.4022 14.2857
25 4JNJ BTN 0.0199 0.40087 15.1786
26 1HV9 COA 0.04692 0.40115 17.8571
27 1P4C FMN 0.03275 0.42003 18.75
28 1YAG ATP 0.002414 0.43423 21.4876
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