Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
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
PDE5A_HUMAN
Ligand General Information  Top
Ligand Name Isobutylmethylxanthine Ligand Info
Canonical SMILES CC(C)CN1C2=C(C(=O)N(C1=O)C)NC=N2
InChI 1S/C10H14N4O2/c1-6(2)4-14-8-7(11-5-12-8)9(15)13(3)10(14)16/h5-6H,4H2,1-3H3,(H,11,12)
InChIKey APIXJSLKIYYUKG-UHFFFAOYSA-N
PubChem Compound ID 3758
Drug Binding Sites of Target  Top
PDB ID: 3JWR      Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87.
Method X-ray diffraction Resolution 2.99 Å Mutation No [1]
PDB Sequence
TRELQSLAAA
546
VVPSAQTLKI
556
TDFSFSDFEL
566
SDLETALCTI
576
RMFTDLNLVQ
586

NFQMKHEVLC
596
RWILSVKKNY
606
RKNVAYHNWR
616
HAFNTAQCMF
626
AALKAGKIQN
636

KLTDLEILAL
646
LIAALSHDLD
656
HRGVNNSYIQ
666
RSEHPLAQLY
676
CHSIMEHHHF
686

DQCLMILNSP
696
GNQILSGLSI
706
EEYKTTLKII
716
KQAILATDLA
726
LYIKRRGEFF
736

ELIRKNQFNL
746
EDPHQKELFL
756
AMLMTACDLS
766
AITKPWPIQQ
776
RIAELVATEF
786

WEQGDLERTV
796
LQQQPIPMMD
806
RNKRDELPKL
816
QVGFIDFVCT
826
QLYEALTHVS
836

EDCFPLLDGC
846
RKNRQKWQAL
856
AEQ
Residue
Distance (Å)
TYR612
3.768
HIS613
3.259
PHE686
3.744
ASP687
3.073
LEU690
3.359
LEU693
3.368
ASN694
3.928
GLN699
3.089
LEU701
2.743
SER702
2.826
GLY703
4.902
LEU704
3.217
SER705
4.493
Residue
Distance (Å)
ILE706
3.939
TYR709
3.440
LEU713
4.441
ASP764
4.283
LEU765
3.322
ALA767
3.749
ILE768
3.794
GLN775
4.556
VAL782
4.204
PHE786
3.747
MET804
4.079
GLN817
3.156
PHE820
3.477
PDB ID: 1RKP      Crystal structure of PDE5A1-IBMX
Method X-ray diffraction Resolution 2.05 Å Mutation Yes [2]
PDB Sequence
EETRELQSLA
544
AAVVPSAQTL
554
KITDFSFSDF
564
ELSDLETALC
574
TIRMFTDLNL
584

VQNFQMKHEV
594
LCRWILSVKK
604
NYRKNVAYHN
614
WRHAFNTAQC
624
MFAALKAGKI
634

QNKLTDLEIL
644
ALLIAALSHD
654
LDHRGVNNSY
664
IQRSEHPLAQ
674
LYCHSIMEHH
684

HFDQCLMILN
694
SPGNQILSGL
704
SIEEYKTTLK
714
IIKQAILATD
724
LALYIKRRGE
734

FFELIRKNQF
744
NLEDPHQKEL
754
FLAMLMTACD
764
LSAITKPWPI
774
QQRLAELVAT
784

EFFDQGDREK
809
KNKIPSMQVG
819
FIDAICLQLY
829
EALTHVSEDC
839
FPLLDGCRKN
849

RQKWQALAEQ
859
Q
Residue
Distance (Å)
TYR612
3.922
HIS613
4.013
VAL660
4.605
LEU725
4.493
ASP764
4.106
LEU765
3.435
ALA767
3.884
Residue
Distance (Å)
ILE768
3.723
GLN775
4.737
VAL782
3.855
PHE786
3.612
MET816
4.076
GLN817
2.685
PHE820
3.314
References  Top
REF 1 Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. EMBO J. 2009 Nov 18;28(22):3613-22.
REF 2 Crystal structures of phosphodiesterases 4 and 5 in complex with inhibitor 3-isobutyl-1-methylxanthine suggest a conformation determinant of inhibitor selectivity. J Biol Chem. 2004 Mar 26;279(13):13095-101.

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