4PH9: Ibuprofen

The structure of Ibuprofen bound to cyclooxygenase-2. Determined by X-ray diffraction at 1.81 Å resolution. Released 26 Nov 2014.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Mus musculus
Chains: 2
Atoms: 10,527
Mol. weight: 132.64 kDa
Ligands: IBP, HEM, BOG, NAG
Released: 26 Nov 2014

Explore 4PH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PH9 contains 88 α-helices and 66 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 44 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	1
β-strand	54-58	5	1
β-strand	64-65	2	2
β-strand	71-72	2	2
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-94	9
α-helix	97-103	7
α-helix	107-122	16
β-strand	131	1	3
β-strand	132	1	4
β-strand	135	1	4
α-helix	140-144	5
β-strand	148	1	5
β-strand	150	1	6
β-strand	151	1	3
α-helix	154-157	4
β-strand	162	1	7
β-strand	165	1	7
α-helix	172-174	3
α-helix	175-178	4
α-helix	179-183	5
β-strand	184	1	8
β-strand	190	1	9
β-strand	195	1	10
β-strand	196	1	11
α-helix	197-207	11
β-strand	213	1	12
β-strand	221	1	5
β-strand	222	1	12
α-helix	232-235	4
α-helix	239-245	7
β-strand	246	1	13
α-helix	252	1
β-strand	253	1	13
α-helix	254	1
β-strand	256-258	3	14
β-strand	261-263	3	14
β-strand	266	1	15
α-helix	267-270	4
α-helix	282-284	3
β-strand	286	1	15
α-helix	293-295	3
α-helix	297-320	24
α-helix	326-344	19
α-helix	345-350	6
α-helix	351-354	4
α-helix	364-367	4
β-strand	379	1	6
α-helix	380-385	6
α-helix	389-391	3
β-strand	396-398	3	16
β-strand	401-403	3	16
α-helix	405-408	4
α-helix	412-429	18
β-strand	431	1	11
α-helix	432	1
β-strand	433	1	9
α-helix	434	1
β-strand	441	1	8
α-helix	443-445	3
α-helix	446-458	13
α-helix	461-463	3
α-helix	464-470	7
α-helix	474-476	3
α-helix	479-483	5
α-helix	487-496	10
α-helix	499-501	3
α-helix	504-510	7
α-helix	512	1
β-strand	513	1	17
β-strand	520	1	17
α-helix	521-536	16
α-helix	539-541	3
α-helix	548-551	4
α-helix	554-561	8
α-helix	565-572	8
β-strand	582	1	10

Chain B: 44 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	18
β-strand	55-58	4	18
β-strand	64-65	2	19
β-strand	71-72	2	19
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-104	8
α-helix	107-122	16
β-strand	131	1	20
β-strand	132	1	21
β-strand	135	1	21
α-helix	140-144	5
β-strand	148	1	22
β-strand	150	1	23
β-strand	151	1	20
α-helix	154-157	4
β-strand	162	1	24
β-strand	165	1	24
α-helix	172-174	3
α-helix	175-178	4
α-helix	179-183	5
β-strand	184	1	25
β-strand	190	1	26
β-strand	195	1	27
β-strand	196	1	28
α-helix	197-207	11
β-strand	213	1	29
β-strand	221	1	22
β-strand	222	1	29
α-helix	232-235	4
α-helix	239-245	7
β-strand	246	1	30
α-helix	252	1
β-strand	253	1	30
α-helix	254	1
β-strand	256-258	3	31
β-strand	261-263	3	31
β-strand	266	1	32
α-helix	267-270	4
α-helix	282-284	3
β-strand	286	1	32
α-helix	293-295	3
α-helix	297-320	24
α-helix	326-344	19
α-helix	345-350	6
α-helix	351-354	4
α-helix	364-367	4
β-strand	379	1	23
α-helix	380-385	6
α-helix	389-391	3
β-strand	396-398	3	33
β-strand	401-403	3	33
α-helix	405-408	4
α-helix	413-429	17
β-strand	431	1	28
α-helix	432	1
β-strand	433	1	26
α-helix	434	1
β-strand	441	1	25
α-helix	443-445	3
α-helix	446-458	13
α-helix	461-463	3
α-helix	464-470	7
α-helix	474-476	3
α-helix	479-483	5
α-helix	487-496	10
α-helix	499-501	3
α-helix	504-510	7
α-helix	512-513	2
α-helix	521-536	16
α-helix	539-541	3
α-helix	548-551	4
α-helix	554-561	8
α-helix	565-572	8
β-strand	582	1	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin G/H synthase 2	A, B	protein	551	Mus musculus	Q05769 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4PH9_1 Prostaglandin G/H synthase 2 (chains A, B)
HHPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYI
LTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRA
LPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFK
TDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV
EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQT
SRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLL
PDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKAS
IDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK
PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNN
VKGCPFTSFNV

Ligands and cofactors

ID	Name	Formula	Copies
IBP	Ibuprofen	C13 H18 O2	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
AKR	Acrylic acid	C3 H4 O2	4

Water and common crystallization additives (EDO) are not listed.

Primary citation

The structure of ibuprofen bound to cyclooxygenase-2. Orlando, B.J., Lucido, M.J., Malkowski, M.G. J Struct Biol (2015) 189:62-66. DOI 10.1016/j.jsb.2014.11.005 · PubMed

Other PDB entries of the same protein (UniProt Q05769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NT1 1.73 Å, High resolution structure of naproxen:COX-2 complex.
5FDQ 1.9 Å, Murine COX-2 S530T mutant
4M10 2.01 Å, Crystal Structure of Murine Cyclooxygenase-2 Complex with Isoxicam
3HS5 2.1 Å, X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of…
3QH0 2.1 Å, X-ray crystal structure of palmitic acid bound to the cyclooxygenase channel of…
4E1G 2.1 Å, X-ray crystal structure of alpha-linolenic acid bound to the cyclooxygenase channel of…
4OTJ 2.11 Å, The complex of murine cyclooxygenase-2 with a conjugate of indomefathin and…
3TZI 2.15 Å, X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of G533V…
8ET0 2.15 Å, Crystal Complex of murine Cyclooxygenase-2 with alpaca nanobody F9
4RUT 2.16 Å, crystal structure of murine cyclooxygenase-2 with 13-methyl-arachidonic Acid
3NTG 2.19 Å, Crystal structure of COX-2 with selective compound 23d-(R)
3LN0 2.2 Å, Structure of compound 5c-S bound at the active site of COX-2

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