-->
Receptor
PDB id Resolution Class Description Source Keywords
3DUU 1.95 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF SAG506-01, ORTHORHOMBIC, TWINNED, CRYSTAL 2 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 B:114;
D:114;
Valid;
Valid;
none;
none;
submit data
238.192 C8 H14 O8 C1[C@...
MG A:112;
C:111;
C:113;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PG4 B:115;
D:115;
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 208 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 (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 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 3DUS - KDO C8 H14 O8 C1[C@H]([C....
7 3DUR - KDO C8 H14 O8 C1[C@H]([C....
8 3DV4 - KDO C8 H14 O8 C1[C@H]([C....
9 3DUU - KDO C8 H14 O8 C1[C@H]([C....
10 3DV6 - KDO C8 H14 O8 C1[C@H]([C....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 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 3T0W - DIW C26 H29 N2 O3 S CC1(c2cccc....
8 3DUS - KDO C8 H14 O8 C1[C@H]([C....
9 3DUR - KDO C8 H14 O8 C1[C@H]([C....
10 3DV4 - KDO C8 H14 O8 C1[C@H]([C....
11 3DUU - KDO C8 H14 O8 C1[C@H]([C....
12 3DV6 - KDO C8 H14 O8 C1[C@H]([C....
13 5XCU - TYR PRO TYR ASP VAL PRO ASP TYR ALA n/a n/a
14 5XCS - TYR PRO TYR ASP VAL PRO ASP TYR ALA n/a n/a
15 2E27 Ka = 2220000000 M^-1 AB0 C16 H24 O8 COCO[C@H]1....
16 1OAR Kd = 40 nM AZN C14 H8 O7 S c1ccc2c(c1....
17 3T0X - DIW C26 H29 N2 O3 S CC1(c2cccc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KDO; Similar ligands found: 12
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 NGE 0.421875 0.688889
11 18D 0.409091 0.673913
12 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 with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 3dur.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4WEY EG6 4.46429
2 3HSS MLA 4.95868
3 1D7O TCL 5.35714
4 1D7O NAD 5.35714
5 4UZI IMD 24.7934
Pocket No.: 2; Query (leader) PDB : 3DUR; Ligand: KDO; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 3dur.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4Z87 GDP 8.03571
2 5FB3 NDP 19.8347
3 3GJB AKG 28.5714
APoc FAQ
Feedback