Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3LY2

Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
A	0007165	biological_process	signal transduction
A	0008081	molecular_function	phosphoric diester hydrolase activity
B	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
B	0007165	biological_process	signal transduction
B	0008081	molecular_function	phosphoric diester hydrolase activity
C	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
C	0007165	biological_process	signal transduction
C	0008081	molecular_function	phosphoric diester hydrolase activity
D	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
D	0007165	biological_process	signal transduction
D	0008081	molecular_function	phosphoric diester hydrolase activity
E	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
E	0007165	biological_process	signal transduction
E	0008081	molecular_function	phosphoric diester hydrolase activity
F	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
F	0007165	biological_process	signal transduction
F	0008081	molecular_function	phosphoric diester hydrolase activity
G	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
G	0007165	biological_process	signal transduction
G	0008081	molecular_function	phosphoric diester hydrolase activity
H	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
H	0007165	biological_process	signal transduction
H	0008081	molecular_function	phosphoric diester hydrolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE Z72 A 1000

Chain	Residue
A	THR345
A	HOH1009
A	HOH1010
A	HOH2120
A	HOH2329
A	HOH2330
A	MET347
A	ASP392
A	LEU393
A	MET431
A	SER442
A	GLN443
A	PHE446
A	HOH1008

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 1001

Chain	Residue
A	HIS238
A	HIS274
A	ASP275
A	ASP392
A	HOH1007
A	HOH1008

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1002

Chain	Residue
A	ASP275
A	HOH1004
A	HOH1005
A	HOH1006
A	HOH1007
A	HOH1010

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 1003

Chain	Residue
A	SER149
A	SER212
A	SER213
A	HOH2079
A	HOH2189

site_id	AC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE Z72 B 1000

Chain	Residue
B	THR345
B	MET347
B	ASP392
B	LEU393
B	ASN395
B	ILE410
B	PHE414
B	MET431
B	SER442
B	GLN443
B	PHE446
B	HOH1009
B	HOH1010
B	HOH2070

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 1001

Chain	Residue
B	HIS238
B	HIS274
B	ASP275
B	ASP392
B	HOH1007
B	HOH1008

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 1002

Chain	Residue
B	ASP275
B	HOH1004
B	HOH1005
B	HOH1006
B	HOH1007
B	HOH1010

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 1003

Chain	Residue
B	PRO146
B	SER149
B	SER212
B	SER213
B	HOH2062
B	HOH2119
B	HOH2327

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE Z72 C 1000

Chain	Residue
C	TYR233
C	THR345
C	MET347
C	ASP392
C	LEU393
C	ILE410
C	MET431
C	SER442
C	GLN443
C	PHE446
C	HOH1006
C	HOH1009
C	HOH1010

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 1001

Chain	Residue
C	HIS238
C	HIS274
C	ASP275
C	ASP392
C	HOH1007
C	HOH1008

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 1002

Chain	Residue
C	ASP275
C	HOH1004
C	HOH1005
C	HOH1006
C	HOH1007
C	HOH1010

site_id	BC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE Z72 D 1000

Chain	Residue
D	SER442
D	GLN443
D	PHE446
D	HOH1006
D	HOH1009
D	HOH1010
D	HOH2127
D	HOH2332
D	TYR233
D	HIS234
D	THR345
D	MET347
D	ASP392
D	LEU393
D	ASN395
D	ILE410
D	MET411
D	MET431

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 1001

Chain	Residue
D	HIS238
D	HIS274
D	ASP275
D	ASP392
D	HOH1007
D	HOH1008

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 1002

Chain	Residue
D	ASP275
D	HOH1004
D	HOH1005
D	HOH1006
D	HOH1007
D	HOH1010

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE Z72 E 1000

Chain	Residue
E	TYR233
E	THR345
E	MET347
E	ASP392
E	LEU393
E	ILE410
E	MET431
E	SER442
E	GLN443
E	PHE446
E	HOH1006
E	HOH1009
E	HOH1010

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN E 1001

Chain	Residue
E	HIS238
E	HIS274
E	ASP275
E	ASP392
E	HOH1007
E	HOH1008

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 1002

Chain	Residue
E	ASP275
E	HOH1004
E	HOH1005
E	HOH1006
E	HOH1007
E	HOH1010

site_id	BC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE Z72 F 1000

Chain	Residue
F	TYR233
F	HIS234
F	THR345
F	MET347
F	ASP392
F	LEU393
F	ASN395
F	ILE410
F	MET411
F	MET431
F	SER442
F	GLN443
F	PHE446
F	HOH1006
F	HOH1008
F	HOH1009
F	HOH1010

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN F 1001

Chain	Residue
F	HIS238
F	HIS274
F	ASP275
F	ASP392
F	HOH1007
F	HOH1008

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 1002

Chain	Residue
F	ASP275
F	HOH1004
F	HOH1005
F	HOH1006
F	HOH1007
F	HOH1010

site_id	CC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE Z72 G 1000

Chain	Residue
G	THR345
G	MET347
G	ASP392
G	LEU393
G	THR407
G	ILE410
G	MET431
G	SER442
G	GLN443
G	PHE446
G	HOH1009
G	HOH1010

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN G 1001

Chain	Residue
G	HIS238
G	HIS274
G	ASP275
G	ASP392
G	HOH1007
G	HOH1008

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG G 1002

Chain	Residue
G	ASP275
G	HOH1004
G	HOH1005
G	HOH1006
G	HOH1007
G	HOH1010

site_id	CC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE Z72 H 1000

Chain	Residue
H	THR345
H	MET347
H	ASP392
H	LEU393
H	THR407
H	ILE410
H	MET431
H	SER442
H	GLN443
H	PHE446
H	HOH1009
H	HOH1010
H	HOH2335

site_id	CC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN H 1001

Chain	Residue
H	HIS238
H	HIS274
H	ASP275
H	ASP392
H	HOH1007
H	HOH1008

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 1002

Chain	Residue
H	ASP275
H	HOH1004
H	HOH1005
H	HOH1006
H	HOH1007
H	HOH1010

Functional Information from PROSITE/UniProt

site_id	PS00126
Number of Residues	12
Details	PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF

Chain	Residue	Details
A	HIS274-PHE285

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15685167","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17727341","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18539455","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1RO6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RO9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XN0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QYL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3D3P","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10846163","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15685167","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17727341","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18539455","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1F0J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RO6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RO9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XN0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2QYL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3D3P","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10846163","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15685167","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18539455","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1F0J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RO6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RO9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XLZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XM6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XMY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XN0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Y2J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3D3P","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15003452","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1ROR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)