3V9B

Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1-[1-(3-Cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4-yl)-ethyl]-1H-pyrazl-3-yl}phenyl)acetamide

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE IHM A 1

Chain	Residue
A	HOH2
A	ASN321
A	PRO322
A	TYR329
A	TRP332
A	THR333
A	PHE340
A	GLN343
A	MET357
A	SER368
A	GLN369
A	HOH65
A	PHE372
A	HOH73
A	TYR159
A	SER208
A	GLU230
A	THR271
A	MET273
A	ASP318

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 501

Chain	Residue
A	HOH24
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH499

---

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 502

Chain	Residue
A	HOH2
A	HOH24
A	HOH30
A	ASP201
A	HOH500
A	HOH503

---

site_id	AC4
Number of Residues	20
Details	BINDING SITE FOR RESIDUE IHM B 1

Chain	Residue
B	HOH4
B	TYR159
B	SER208
B	GLU230
B	THR271
B	MET273
B	ASN321
B	PRO322
B	TYR329
B	TRP332
B	THR333
B	ILE336
B	PHE340
B	GLN343
B	CYS358
B	SER368
B	GLN369
B	PHE372
B	HOH477
B	HOH482

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 503

Chain	Residue
B	HOH23
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH493

---

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 504

Chain	Residue
B	HOH4
B	HOH22
B	HOH23
B	HOH67
B	ASP201
B	HOH494

---

site_id	AC7
Number of Residues	18
Details	BINDING SITE FOR RESIDUE IHM C 1

Chain	Residue
C	HOH19
C	TYR159
C	SER208
C	THR271
C	MET273
C	ASP318
C	ASN321
C	TYR329
C	TRP332
C	THR333
C	ILE336
C	PHE340
C	GLN343
C	SER368
C	GLN369
C	PHE372
C	HOH452
C	HOH464

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 505

Chain	Residue
C	HOH29
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH501

---

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 506

Chain	Residue
C	HOH19
C	HOH29
C	HOH36
C	ASP201
C	HOH500
C	HOH502

---

site_id	BC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE IHM D 1

Chain	Residue
D	MET273
D	ASN321
D	PRO322
D	TYR329
D	TRP332
D	THR333
D	ILE336
D	PHE340
D	GLN343
D	MET357
D	CYS358
D	SER368
D	GLN369
D	PHE372
D	HOH449
D	HOH477
D	HOH14
D	TYR159
D	SER208
D	GLU230
D	THR271

---

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 507

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH439
D	HOH505

---

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 508

Chain	Residue
D	HOH14
D	ASP201
D	HOH439
D	HOH506
D	HOH509
D	HOH510

---

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	4
Details	ACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343

Chain	Residue	Details
A	HIS160
B	HIS160
C	HIS160
D	HIS160

---

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7

Chain	Residue	Details
A	HIS160
D	HIS160
D	ASN321
D	GLN369
A	ASN321
A	GLN369
B	HIS160
B	ASN321
B	GLN369
C	HIS160
C	ASN321
C	GLN369

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:2PW3

Chain	Residue	Details
A	HIS164
B	HIS164
C	HIS164
D	HIS164

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:1XOR, ECO:0007744|PDB:2PW3

Chain	Residue	Details
A	HIS200
A	ASP318
B	HIS200
B	ASP318
C	HIS200
C	ASP318
D	HIS200
D	ASP318

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW

Chain	Residue	Details
A	ASP201
A	PHE372
B	ASP201
B	PHE372
C	ASP201
C	PHE372
D	ASP201
D	PHE372

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)

Chain	Residue	Details
A	LYS85
B	LYS85
C	LYS85
D	LYS85

---