Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1Y2K

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester

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	6
Details	BINDING SITE FOR RESIDUE ZN A 1001

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH1007
A	HOH1008

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1002

Chain	Residue
A	HOH1005
A	HOH1006
A	HOH1007
A	ASP201
A	HOH1003
A	HOH1004

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 1001

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH2007
B	HOH2008

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 1002

Chain	Residue
B	ASP201
B	HOH2003
B	HOH2004
B	HOH2005
B	HOH2006
B	HOH2007

site_id	AC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE 7DE B 601

Chain	Residue
B	TYR159
B	THR271
B	MET273
B	ASP318
B	LEU319
B	ASN321
B	THR333
B	ILE336
B	GLN369
B	PHE372
B	HOH2018
B	HOH2025
B	HOH2220

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 7DE A 602

Chain	Residue
A	TYR159
A	THR271
A	MET273
A	ASP318
A	LEU319
A	ASN321
A	THR333
A	ILE336
A	GLN369
A	PHE372
A	HOH1016

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 701

Chain	Residue
A	PRO411
B	GLU366
B	TYR406
B	HOH2032

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 702

Chain	Residue
A	LYS262
A	ILE265
A	ASP266
A	HOH1025
B	HOH2184

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 704

Chain	Residue
A	ASN209
A	GLN210
A	HOH1014
A	HOH1034
A	HOH1038
A	HOH1046

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 706

Chain	Residue
A	HOH1088
B	EDO728
B	HOH2104

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 707

Chain	Residue
A	GLU150
A	ASP151
A	TYR153
A	ASN162
A	HOH1075
A	HOH1148
A	HOH1204
B	GLN407

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 708

Chain	Residue
B	SER208
B	PHE340
B	GLN343
B	PRO356

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 709

Chain	Residue
B	LYS255
B	GLN258
B	SER259

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 712

Chain	Residue
A	PRO179
A	SER295
A	GLY296
A	HIS389
A	ASP391

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 715

Chain	Residue
A	ASN115
A	ALA155
A	ASN162
A	ILE163
A	HOH1148
A	HOH1171

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 716

Chain	Residue
A	LEU175
A	THR178
A	TRP384
A	ASP391
A	ALA392
A	HOH1081

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 717

Chain	Residue
B	ARG261
B	EDO718
B	HOH2072
B	HOH2110
B	ARG257

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 718

Chain	Residue
B	ARG257
B	GLN258
B	ARG261
B	EDO717
B	HOH2206

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 719

Chain	Residue
A	ALA183
A	VAL184
A	HOH1128
B	GLY114
B	ASN115
B	ARG116

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 720

Chain	Residue
A	PHE238
A	PHE249
A	ARG257
A	ARG261
A	HOH1060
A	HOH1131

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 722

Chain	Residue
A	SER208
A	PHE340
A	PRO356
A	HOH1056
A	HOH1236

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 723

Chain	Residue
A	SER208
A	ASN209
A	LEU229
A	GLU230
A	ASP272
A	MET273
A	HOH1030

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 724

Chain	Residue
A	VAL236
A	LYS239
A	HOH1018

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 725

Chain	Residue
A	ASN224
B	LYS262
B	ILE265
B	ASP266
B	HOH2041

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO B 726

Chain	Residue
A	HOH1108
B	GLU150
B	ASP151
B	TYR153
B	ASN162
B	EDO734
B	HOH2010
B	HOH2132
B	HOH2139
B	HOH2167

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 727

Chain	Residue
B	ASN402
B	TRP405
B	HOH2033

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 728

Chain	Residue
A	ARG330
B	EDO706
B	HOH2014
B	HOH2061
B	HOH2219

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 729

Chain	Residue
A	ASP156
A	PRO205
A	HOH1019
A	HOH1033

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 730

Chain	Residue
B	ASP156
B	PRO205
B	ARG342
B	HOH2022
B	HOH2029
B	HOH2227

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 731

Chain	Residue
A	LYS367
A	GLN407
A	ILE410
A	HOH1052

site_id	DC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 732

Chain	Residue
A	ILE213
A	ASN216
A	SER217
A	ALA220
A	LEU221
A	ASP225
A	HOH1040
B	ARG261

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 733

Chain	Residue
A	HIS154
A	ASP203
A	PRO205
A	LEU219

site_id	DC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 734

Chain	Residue
B	ASN115
B	ALA155
B	ASN162
B	ILE163
B	EDO726
B	HOH2114
B	HOH2167
B	HOH2169

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 735

Chain	Residue
B	MET277
B	LEU280
B	ALA281
B	LYS284

site_id	DC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 736

Chain	Residue
A	ARG348
A	LYS360
A	HIS361

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 737

Chain	Residue
B	ASP282
B	MET286
B	GLN308

site_id	EC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 738

Chain	Residue
A	ASP397
A	GLU400
A	ASP401
B	ARG108

site_id	EC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 739

Chain	Residue
A	ARG335
A	GLU338
A	HOH1172
A	HOH1174
A	HOH1191

site_id	EC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 740

Chain	Residue
A	ASP151
A	HIS152
B	GLY371
B	ASP374
B	TYR375
B	HOH2124

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)