Receptor
PDB id Resolution Class Description Source Keywords
3ODU 2.5 Å EC: 3.2.1.17 THE 2.5 A STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPL SMALL MOLECULE ANTAGONIST IT1T HOMO SAPIENS, ENTEROBACTERIA PHAGE T4 STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE ACTECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D 7TM PROTEIN-COUPLED RECEPTOR GPCR SIGNAL TRANSDUCTION HYDROLCANCER HIV-1 CO-RECEPTOR CHEMOKINE CXCL12 SDF1 ISOTHIOCHIMERA T4L FUSION MEMBRANE PROTEIN TRANSMEMBRANE SINGNPROTEIN PSI-BIOLOGY GPCR NETWORK SIGNALING PROTEIN
Ref.: STRUCTURES OF THE CXCR4 CHEMOKINE GPCR WITH SMALL-M AND CYCLIC PEPTIDE ANTAGONISTS. SCIENCE V. 330 1066 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ITD A:1500;
B:1500;
 Valid;
Valid;
 none;
none;
 submit data
406.651 C21 H34 N4 S2 CC1(C...
OLA A:1610;
B:1605;
B:1606;
B:1607;
B:1608;
B:1609;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
282.461 C18 H34 O2 CCCCC...
OLC A:1600;
A:1603;
A:1604;
B:1601;
B:1602;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
356.54 C21 H40 O4 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ODU 2.5 Å EC: 3.2.1.17 THE 2.5 A STRUCTURE OF THE CXCR4 CHEMOKINE RECEPTOR IN COMPL SMALL MOLECULE ANTAGONIST IT1T HOMO SAPIENS, ENTEROBACTERIA PHAGE T4 STRUCTURAL GENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE ACTECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE ATCG3D 7TM PROTEIN-COUPLED RECEPTOR GPCR SIGNAL TRANSDUCTION HYDROLCANCER HIV-1 CO-RECEPTOR CHEMOKINE CXCL12 SDF1 ISOTHIOCHIMERA T4L FUSION MEMBRANE PROTEIN TRANSMEMBRANE SINGNPROTEIN PSI-BIOLOGY GPCR NETWORK SIGNALING PROTEIN
Ref.: STRUCTURES OF THE CXCR4 CHEMOKINE GPCR WITH SMALL-M AND CYCLIC PEPTIDE ANTAGONISTS. SCIENCE V. 330 1066 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3ODU - ITD C21 H34 N4 S2 CC1(CN2C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 3ODU - ITD C21 H34 N4 S2 CC1(CN2C(=....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 2RH1 - CAU C18 H22 N2 O2 CC(C)NC[C@....
2 5D5A - CLR C27 H46 O CC(C)CCC[C....
3 6PS3 Ki = 0.166 nM CVD C24 H26 N2 O4 COc1ccccc1....
4 6PS2 Ki = 1 nM JTZ C15 H23 N O2 CC(C)NC[C@....
5 3ODU - ITD C21 H34 N4 S2 CC1(CN2C(=....
6 5X93 ic50 = 150 nM K87 C36 H38 N6 O6 S Cc1cccc(c1....
7 4PHU Kd = 12.04 nM 2YB C29 H32 O7 S Cc1cc(cc(c....
8 5TZR - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ITD; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ITD 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: ITD; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ODU; Ligand: ITD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3odu.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3ODU; Ligand: ITD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3odu.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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