Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T94879 | Target Info | |||
| Target Name | HUMAN phosphodiesterase type 5 (PDE5) | ||||
| Synonyms | cGMP-specific 3',5'-cyclic phosphodiesterase; PDE5A; CGMP-binding cGMP-specific phosphodiesterase; CGB-PDE | ||||
| Gene Name | PDE5A | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Vardenafil | Ligand Info | |||
| Canonical SMILES | CCCC1=NC(=C2N1N=C(NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)CC)OCC)C | ||||
| InChI | 1S/C23H32N6O4S/c1-5-8-20-24-16(4)21-23(30)25-22(26-29(20)21)18-15-17(9-10-19(18)33-7-3)34(31,32)28-13-11-27(6-2)12-14-28/h9-10,15H,5-8,11-14H2,1-4H3,(H,25,26,30) | ||||
| InChIKey | SECKRCOLJRRGGV-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 135400189 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1XP0 Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil | ||||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | Yes | [1] |
| PDB Sequence |
EEETRELQSL
543 AAAVVPSAQT553 LKITDFSFSD563 FELSDLETAL573 CTIRMFTDLN583 LVQNFQMKHE 593 VLCRWILSVK603 KNYRKNVAYH613 NWRHAFNTAQ623 CMFAALKAGK633 IQNKLTDLEI 643 LALLIAALSH653 DLDHPGVSNQ663 FLINTNSELA673 LMYNDESVLE682 HHHFDQCLMI 692 LNSPGNQILS702 GLSIEEYKTT712 LKIIKQAILA722 TDLALYIKRR732 GEFFELIRKN 742 QFNLEDPHQK752 ELFLAMLMTA762 CDLSAITKPW772 PIQQRIAELV782 ATEFFDQGDR 792 ERKELNIEPT802 DLMNREKKNK812 IPSMQVGFID822 AICLQLYEAL832 THVSEDCFPL 842 LDGCRKNRQK852 WQALAE
|
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TYR612
3.717
HIS613
4.245
LEU725
4.056
ASP764
4.992
LEU765
3.863
ALA767
3.759
ILE768
3.806
GLN775
4.249
ILE778
4.639
ALA779
3.771
|
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| PDB ID: 3B2R Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil | ||||||
| Method | X-ray diffraction | Resolution | 2.07 Å | Mutation | No | [2] |
| PDB Sequence |
GSHMEETREL
540 QSLAAAVVPS550 AQTLKITDFS560 FSDFELSDLE570 TALCTIRMFT580 DLNLVQNFQM 590 KHEVLCRWIL600 SVKKNYRKNV610 AYHNWRHAFN620 TAQCMFAALK630 AGKIQNKLTD 640 LEILALLIAA650 LSHDLDHRGV660 CHSIMEHHHF686 DQCLMILNSP696 GNQILSGLSI 706 EEYKTTLKII716 KQAILATDLA726 LYIKRRGEFF736 ELIRKNQFNL746 EDPHQKELFL 756 AMLMTACDLS766 AITKPWPIQQ776 RIAELVATEF786 FDQGDKKNKI813 PSMQVGFIDA 823 ICLQLYEALT833 HVSEDCFPLL843 DGCRKNRQKW853 QALAEQQ
|
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|
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| PDB ID: 1UHO Crystal structure of Human Phosphodiesterase 5 complexed with Vardenafil(Levitra) | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
TRELQSLAAA
546 VVPSAQTLKI556 TDFSFSDFEL566 SDLETALCTI576 RMFTDLNLVQ586 NFQMKHEVLC 596 RWILSVKKNY606 RKNVAYHNWR616 HAFNTAQCMF626 AALKAGKIQN636 KLTDLEILAL 646 LIAALSHDLD656 HRGVNNSYYC677 HSIMEHHHFD687 QCLMILNSPG697 NQILSGLSIE 707 EYKTTLKIIK717 QAILATDLAL727 YIKRRGEFFE737 LIRKNQFNLE747 DPHQKELFLA 757 MLMTACDLSA767 ITKPWPIQQR777 IAELVATEFF787 DQGDRERKEL797 NIEPTDLMNR 807 EKKNKIPSMQ817 VGFIDAICLQ827 LYEALTHVSE837 DCFPLLDGCR847 KNRQKWQALA 857 EQQ
|
|||||
|
|
TYR612
3.321
HIS613
3.212
ASN661
4.391
SER663
4.005
TYR664
2.976
LEU725
4.960
LEU765
4.693
ALA767
4.252
ILE768
4.095
GLN775
4.293
ALA779
3.477
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure. 2004 Dec;12(12):2233-47. | ||||
| REF 2 | Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil. Mol Pharmacol. 2008 Jan;73(1):104-10. | ||||
| REF 3 | Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules. Nature. 2003 Sep 4;425(6953):98-102. | ||||
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