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 15 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 10 families.
1 3ODU - ITD C21 H34 N4 S2 CC1(CN2C(=....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2RH1 - CAU C18 H22 N2 O2 CC(C)NC[C@....
2 5D5A - N9S C12 H22 O11 C([C@@H]1[....
3 3ODU - ITD C21 H34 N4 S2 CC1(CN2C(=....
4 5X93 ic50 = 150 nM K87 C36 H38 N6 O6 S Cc1cccc(c1....
5 4PHU Kd = 16 nM 2YB C29 H32 O7 S Cc1cc(cc(c....
6 5TZR - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ITD; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ITD 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ODU; Ligand: ITD; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 3odu.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I54 1C1 0.04053 0.4036 1.41643
2 1OFD AKG 0.02157 0.42178 1.59363
3 1OFD FMN 0.02368 0.4217 1.59363
4 4N8I COA 0.03138 0.4059 1.99203
5 4Q3S X7A 0.01668 0.40575 2.07792
6 1ELJ GLC GLC GLC 0.02116 0.40243 2.62467
7 5L4L 7OX 0.04028 0.41101 2.63158
8 5L4L NAP 0.02741 0.40631 2.63158
9 1YID ATP 0.003846 0.43324 3.1339
10 4OKZ 3E9 0.02558 0.40645 3.28767
11 3R5Z F42 0.01782 0.41614 4.13793
12 1OYB HBA 0.03626 0.40255 4.5
13 3ZX4 2M8 0.01129 0.41 6.94981
14 2YVJ NAI 0.01947 0.40612 7.35294
15 1RL4 BL5 0.011 0.4331 12.234
Pocket No.: 2; Query (leader) PDB : 3ODU; Ligand: ITD; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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