Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6FEB

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1086

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue EDO A 501

Chain	Residue
A	LYS262
A	ASP266
B	HOH611
B	HOH614

site_id	AC2
Number of Residues	5
Details	binding site for residue EDO A 502

Chain	Residue
A	SER208
A	SER355
A	PRO356
A	CYS358
A	HOH655

site_id	AC3
Number of Residues	2
Details	binding site for residue EDO A 503

Chain	Residue
A	GLU182
B	LYS255

site_id	AC4
Number of Residues	6
Details	binding site for residue EDO A 504

Chain	Residue
A	LEU175
A	THR178
A	TRP384
A	ASP391
A	ILE395
A	HOH613

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 505

Chain	Residue
A	ASP391
B	THR134
B	ASN251
B	GLN256

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 506

Chain	Residue
A	ASP247
A	PHE249
A	GLN250
A	ARG257

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO A 507

Chain	Residue
A	GLN210
A	HOH625
A	HOH631
A	HOH653

site_id	AC8
Number of Residues	5
Details	binding site for residue EDO A 508

Chain	Residue
A	ASP266
A	LEU269
A	LYS275
A	GLN311
A	HOH612

site_id	AC9
Number of Residues	2
Details	binding site for residue EDO A 509

Chain	Residue
A	ASN278
A	ASP282

site_id	AD1
Number of Residues	1
Details	binding site for residue EDO A 510

Chain	Residue
A	ASP374

site_id	AD2
Number of Residues	10
Details	binding site for residue D5Z A 511

Chain	Residue
A	MET273
A	ASN321
A	ILE336
A	MET337
A	PRO356
A	MET357
A	GLN369
A	PHE372
A	ILE376
A	HOH683

site_id	AD3
Number of Residues	9
Details	binding site for residue D5Z A 512

Chain	Residue
A	GLN127
A	LEU132
A	LYS133
A	LYS136
A	ILE137
A	GLU288
A	THR289
A	VAL292
A	THR293

site_id	AD4
Number of Residues	6
Details	binding site for residue MG A 513

Chain	Residue
A	ASP201
A	HOH621
A	HOH622
A	HOH648
A	HOH665
A	HOH728

site_id	AD5
Number of Residues	6
Details	binding site for residue ZN A 514

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH621
A	HOH693

site_id	AD6
Number of Residues	7
Details	binding site for residue EPE A 515

Chain	Residue
A	HIS105
A	VAL106
A	PHE107
A	ARG108
A	GLU111
A	LEU328
A	GLN331

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO A 516

Chain	Residue
A	ASN231
A	HOH688
A	HOH714
B	ASN231

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO B 501

Chain	Residue
A	HOH614
A	HOH636
B	LYS262
B	ASP266

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO B 502

Chain	Residue
B	SER208
B	SER355
B	PRO356
B	CYS358

site_id	AE1
Number of Residues	6
Details	binding site for residue EDO B 503

Chain	Residue
A	PRO179
A	ALA180
A	GLU182
B	THR253
B	LYS254
B	LYS255

site_id	AE2
Number of Residues	5
Details	binding site for residue EDO B 504

Chain	Residue
B	HIS152
B	THR215
B	SER217
B	GLU243
B	ARG350

site_id	AE3
Number of Residues	4
Details	binding site for residue EDO B 505

Chain	Residue
B	ASP203
B	PRO205
B	LEU219
B	HIS154

site_id	AE4
Number of Residues	4
Details	binding site for residue EDO B 506

Chain	Residue
B	ASN115
B	GLU150
B	TYR153
B	ASN162

site_id	AE5
Number of Residues	6
Details	binding site for residue EDO B 507

Chain	Residue
B	LEU175
B	THR178
B	TRP384
B	VAL388
B	ASP391
B	ILE395

site_id	AE6
Number of Residues	9
Details	binding site for residue D5Z B 508

Chain	Residue
B	MET273
B	LEU319
B	ASN321
B	ILE336
B	MET357
B	GLN369
B	PHE372
B	ILE376
B	HOH667

site_id	AE7
Number of Residues	6
Details	binding site for residue MG B 509

Chain	Residue
B	ASP201
B	HOH603
B	HOH628
B	HOH632
B	HOH664
B	HOH687

site_id	AE8
Number of Residues	6
Details	binding site for residue ZN B 510

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH603
B	HOH672

site_id	AE9
Number of Residues	7
Details	binding site for residue EPE B 511

Chain	Residue
B	HIS105
B	VAL106
B	PHE107
B	ARG108
B	GLU111
B	LEU328
B	GLN331

site_id	AF1
Number of Residues	3
Details	binding site for residue EDO B 512

Chain	Residue
B	PHE238
B	ARG257
B	HOH636

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	HIS200-PHE211

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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