Uniprot accession / id : Q01065  OR   Uniprot accession / id : Q01064
 
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Entry Information
Entry status  (1)
REL
(7)
 
Experimental methods  (1)
X-ray diffraction
(7)
 
Authors  (88)
Am Ende CW
(3)
Humphrey JM
(3)
Liras S
(3)
Menniti FS
(3)
Pandit J
(3)
Aertgeerts K
(2)
Allerston CK
(2)
Andersen CB
(2)
Arnold EP
(2)
Augustin M
(2)
Barido R
(2)
Barker R
(2)
Botrous I
(2)
Branstetter B
(2)
Breitenbucher JG
(2)
Cedervall EP
(2)
Chun LE
(2)
Dyck B
(2)
Edwards TE
(2)
Evdokimova A
(2)
Evdomikov A
(2)
Gharbaoui T
(2)
Gomez L
(2)
Head JL
(2)
Hudson AR
(2)
Jenkinsonb S
(2)
Lebel LA
(2)
Lee D
(2)
Limberis J
(2)
Mansour M
(2)
Marrone T
(2)
Massari ME
(2)
Neul D
(2)
Peters M
(2)
Petroski R
(2)
Samas B
(2)
Schmelzer K
(2)
Sebring K
(2)
Simons S
(2)
Simons SP
(2)
Sridhar V
(2)
Tabatabaei A
(2)
Vajdos F
(2)
Xu R
(2)
Yang EX
(2)
Zhou X
(2)
Artis DR
(1)
Beard JD
(1)
Becker SL
(1)
Bollag G
(1)
Card GL
(1)
Chappie TA
(1)
Davis RE
(1)
Fong D
(1)
Gillette S
(1)
Hendrick JP
(1)
Heyser CJ
(1)
Hsieh D
(1)
Ida K
(1)
Jenkinson S
(1)
Kim S-H
(1)
Kim SH
(1)
Lane W
(1)
Li P
(1)
Liras JL
(1)
Milburn MV
(1)
Movsesian M
(1)
Neiman J
(1)
Orozco C
(1)
Schlessinger J
(1)
Snell G
(1)
Snyder GL
(1)
Sogabe S
(1)
Suzuki Y
(1)
Vajdos FF
(1)
Vandeput F
(1)
Vanover KE
(1)
Wennogle LP
(1)
West BL
(1)
Yang E
(1)
Yao W
(1)
Zhang C
(1)
Zhang KY
(1)
Zhang KYJ
(1)
Zhang L
(1)
Zhao J
(1)
Zheng H
(1)
Zhu H
(1)
 
Homo / hetero assembly  (1)
homo
(7)
 
Assembly composition  (1)
protein structure
(7)
 
Assembly polymer count  (1)
monomer
(7)
 
Resolution distribution
1.5 - 2
(5)
2.0 - 2.5
(2)
 
Release year distribution
2000 - 2005
(1)
2010 - 2015
(2)
2015 - 2020
(4)
 
Journal  (3)
J Med Chem
(4)
MEDCHEMCOMM
(2)
Mol Cell
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(7)
 
Organism name  (1)
Homo sapiens
(7)
 
Molecule name  (3)
63 kDa Cam-PDE
(7)
Cam-PDE 1B
(7)
Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
(7)
 
Molecule type  (1)
Protein
(7)
 
Gene names  (2)
PDE1B
(7)
PDES1B
(7)
 
Interacting ligands  (9)
MG : MAGNESIUM ION
(7)
ZN : ZINC ION
(7)
0NY : 7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl)propan-2-yl]quinazolin-4-amine
(2)
0NK : 6,7,8-trimethoxy-N-(pentan-3-yl)quinazolin-4-amine
(1)
4QJ : (11R,15S)-4-{[4-(6-fluoropyridin-2-yl)phenyl]methyl}-8-methyl-5-(phenylamino)-1,3,4,8,10-pentaazatetracyclo[7.6.0.02,6.011,15]pentadeca-2,5,9-trien-7-one
(1)
8HM : 6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
(1)
8HP : 6-[(4-chlorophenyl)methyl]-8,9,10,11-tetrahydro[1]benzothieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one
(1)
GOL : GLYCEROL
(1)
SO4 : SULFATE ION
(1)
 
Function and Biology
EC number / name  (1)
3.1.4.17 : 3',5'-cyclic-nucleotide phosphodiesterase
(7)
 
Biological function  (2)
3',5'-cyclic-nucleotide phosphodiesterase activity
(7)
phosphoric diester hydrolase activity
(7)
 
Biological process  (1)
signal transduction
(7)
 
Sequence and Structure classification
SCOP fold  (1)
HD-domain/PDEase-like
(1)
 
SCOP family  (1)
PDEase
(1)
 
CATH class  (1)
Mainly Alpha
(7)
 
CATH topology  (1)
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(7)
 
Pfam accession / name  (1)
PF00233 : PDEase_I
(7)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(7)
 
Diffraction radiation source type  (1)
Synchrotron
(7)
 
Diffraction source  (4)
APS BEAMLINE 21-ID-D
(3)
ALS BEAMLINE 5.0.2
(2)
ALS BEAMLINE 5.0.3
(1)
ALS BEAMLINE 8.3.1
(1)
 
Synchrotron site  (2)
ALS
(4)
APS
(3)
 
Diffraction detector type  (2)
CCD
(5)
Pixel
(2)
 
Refinement software  (3)
REFMAC
(3)
BUSTER
(2)
PHENIX
(2)
 
Representative Structures
Representative Structures
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Entries 1 to 7 of 7
Entries 1 to 7 of 7
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Crystal structure of human PDE1B with inhibitor 3
Ida K, Lane W, Snell G, Sogabe S
J Med Chem (2016) [PMID: 26789933  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    GOL    ZN    SO4    ZN    MG   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
1.9Å resolution
Released: 3 Feb 2016
Model geometry
Fit model/data
5b25
5b25
5b25
Crystal structure of human PDE1B catalytic domain in complex with inhibitor 3 (6-(4-chlorobenzyl)-8,9,10,11-tetrahydrobenzo[4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one)
Cedervall EP, Allerston CK, Xu R, Sridhar V, Barker R, Aertgeerts K
J Med Chem (2017) [PMID: 28406621  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: 8HP    MG    ZN    ZN    MG    8HP   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
2.04Å resolution
Released: 26 Apr 2017
Model geometry
Fit model/data
5up0
5up0
5up0
Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16j (6-(4-Methoxybenzyl)-9-((tetrahydro-2H-pyran-4-yl)methyl)-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one)
Cedervall EP, Allerston CK, Xu R, Sridhar V, Barker R, Aertgeerts K
J Med Chem (2017) [PMID: 28406621  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ZN    8HM    ZN    MG    8HM   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
1.82Å resolution
Released: 26 Apr 2017
Model geometry
Fit model/data
5uoy
5uoy
5uoy
PDE1b complexed with compound 3S
Vajdos FF
J Med Chem (2018) [PMID: 29718668  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ZN    ZN    MG    0NY   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
1.9Å resolution
Released: 30 May 2018
Model geometry
Fit model/data
5w6e
5w6e
5w6e
Crystal structure of human PDE1B bound to inhibitor 19A (7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl)propan-2-yl]quinazolin-4-amine)
Pandit J, Evdomikov A, Mansour M, Simons S
MEDCHEMCOMM (2014)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ZN    ZN    MG    0NY   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
1.9Å resolution
Released: 16 Jul 2014
Model geometry
Fit model/data
4npw
4npw
4npw
Crystal structure of human PDE1B bound to inhibitor 7A (6,7,8-trimethoxy-N-(pentan-3-yl)quinazolin-4-amine)
Pandit J, Evdomikov A, Mansour M, Simons S
MEDCHEMCOMM (2014)
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ZN    0NK    ZN    MG    0NK   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
2.4Å resolution
Released: 16 Jul 2014
Model geometry
Fit model/data
4npv
4npv
4npv
Catalytic Domain Of Human Phosphodiesterase 1B
Zhang KYJ, Card GL, Suzuki Y, Artis DR, Fong D, Gillette S, Hsieh D, Neiman J, West BL, Zhang C, Milburn MV, Kim S-H, Schlessinger J, Bollag G
Mol Cell (2004) [PMID: 15260978  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: MG    ZN    ZN    MG   
Modified residues: CME    CME   
Assembly name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169511 (Preferred)   search this ID
PDBe-KB: Q01064   
X-ray diffraction
1.77Å resolution
Released: 3 Aug 2004
Model geometry
Fit model/data
1taz
1taz
1taz
Entries 1 to 7 of 7
Entries 1 to 7 of 7