Display Options: Structure:  

Goto PDB code:

3D presentation of molecule is powered by 3Dmol, which supports all modern browsers and mobile devices via WebGL.

Hold mouse button: left to rotate,middle to shift,right to zoom

Related entries of code: 3v9b
Entries with 90% protein sequence similarity cutoff in PDBbind
PDB CodeCheck DatabaseProtein Sequence Similarity
1mkdRCSB PDB    PDBbind328aa, >1MKD:L|PDBID|CHAIN|... at 99%
1q9mRCSB PDB    PDBbind360aa, >1Q9M:D|PDBID|CHAIN|... at 92%
1oynRCSB PDB    PDBbind360aa, >1OYN:D|PDBID|CHAIN|... at 92%
1xomRCSB PDB    PDBbind349aa, >1XOM:B|PDBID|CHAIN|... at 94%
1xonRCSB PDB    PDBbind349aa, >1XON:B|PDBID|CHAIN|... at 94%
1xoqRCSB PDB    PDBbind349aa, >1XOQ:B|PDBID|CHAIN|... at 94%
1xorRCSB PDB    PDBbind349aa, >1XOR:B|PDBID|CHAIN|... at 94%
1y2bRCSB PDB    PDBbind349aa, >1Y2B:B|PDBID|CHAIN|... at 94%
1y2cRCSB PDB    PDBbind349aa, >1Y2C:B|PDBID|CHAIN|... at 94%
1y2dRCSB PDB    PDBbind349aa, >1Y2D:B|PDBID|CHAIN|... at 94%
1y2eRCSB PDB    PDBbind349aa, >1Y2E:B|PDBID|CHAIN|... at 94%
1y2kRCSB PDB    PDBbind349aa, >1Y2K:B|PDBID|CHAIN|... at 94%
1zknRCSB PDB    PDBbind334aa, >1ZKN:D|PDBID|CHAIN|... at 100%
2fm0RCSB PDB    PDBbind361aa, >2FM0:D|PDBID|CHAIN|... at 92%
2fm5RCSB PDB    PDBbind361aa, >2FM5:D|PDBID|CHAIN|... at 92%
2qynRCSB PDB    PDBbind328aa, >2QYN:B|PDBID|CHAIN|... at 99%
3g4gRCSB PDB    PDBbind421aa, >3G4G:D|PDBID|CHAIN|... at 100%
3sl4RCSB PDB    PDBbind361aa, >3SL4:D|PDBID|CHAIN|... at 92%
3sl5RCSB PDB    PDBbind359aa, >3SL5:D|PDBID|CHAIN|... at 93%
3sl8RCSB PDB    PDBbind361aa, >3SL8:D|PDBID|CHAIN|... at 92%
4wcuRCSB PDB    PDBbind359aa, >4WCU:D|PDBID|CHAIN|... at 93%
5k1iRCSB PDB    PDBbind326aa, >5K1I:H|PDBID|CHAIN|... at 100%
5k32RCSB PDB    PDBbind325aa, >5K32:B|PDBID|CHAIN|... at 99%
5wqaRCSB PDB    PDBbind334aa, >5WQA:B|PDBID|CHAIN|... at 100%
6f6uRCSB PDB    PDBbind343aa, >6F6U:B|PDBID|CHAIN|... at 99%
6f8rRCSB PDB    PDBbind343aa, >6F8R:B|PDBID|CHAIN|... at 99%
6f8tRCSB PDB    PDBbind343aa, >6F8T:B|PDBID|CHAIN|... at 99%
6f8uRCSB PDB    PDBbind343aa, >6F8U:B|PDBID|CHAIN|... at 99%
6f8vRCSB PDB    PDBbind343aa, >6F8V:B|PDBID|CHAIN|... at 99%
6f8wRCSB PDB    PDBbind343aa, >6F8W:B|PDBID|CHAIN|... at 99%
6f8xRCSB PDB    PDBbind343aa, >6F8X:B|PDBID|CHAIN|... at 99%
6fdcRCSB PDB    PDBbind343aa, >6FDC:B|PDBID|CHAIN|... at 99%
Complexes with the same small molecule ligand
PDB CodeCheck DatabaseLigand Name
No complexes with the same small molecule ligand are found!

Entry Information
PDB ID3v9b
Complex TypeProtein-Ligand
PDBbind Subsetgeneral set
Protein NamecAMP-specific 3',5'-cyclic phosphodiesterase 4D
Ligand NameIHM
EC.Number E.C.
Resolution 2.1(Å)
Affinity (Kd/Ki/IC50)IC50=0.5nM
Release Year2012
Protein/NA SequenceCheck fasta file
Primary Reference(2012) Org.Biomol.Chem. Vol. 10: pp. 2613-2620
Ligand Properties
Formula C29H28F2N4O4
Molecular Weight 534.554
Exact Mass 534.208
No. of atoms 67
No. of bonds 71
Polar Surface Area 90.84
LOGP Value 4.23      (Computed with XLOGP3)
6.23      (Computed with Open Babel)
Drug likenessNo. of Hydrogen Bond Donors: 1
No. of Hydrogen Bond Acceptors: 3
No. of Rotatable Bonds: 12
No. of Nitrogen and Oxygen Atoms: 8
No. of Rings: 5
Canonical SMILES
InChI String

Links to External Databases
RCSB PDBThe mother database
PDBsumEnhanced annotations on PDB entries
PubchemComprehensive collection of chemical and biological data
UniProtKB ACUniProt accession number (AC): Q08499  
Entrez Gene IDNCBI Entrez Gene ID: 5144  
ASDInformation of known allosteric effects of PDB entries

This site has been visited times since Nov 2007.

Address: 826 Zhangheng Road, Shanghai 201203, People's Republic of China      ICP NO: Shanghai-05005485-2
Group Leader: wangrx@fudan.edu.cn      Tel: +86-21-54925128      Webmaster: liuhai@mail.sioc.ac.cn
Copyright ©2007-2020    Department of Medicinal Chemistry, School of Pharmacy, Fudan University, P.R. China