5IKQ: Meclofenamic Acid

The Structure of Meclofenamic Acid Bound to Human Cyclooxygenase-2. Determined by X-ray diffraction at 2.41 Å resolution. Released 25 May 2016.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,671
Mol. weight: 131.57 kDa
Ligands: BOG, JMS, COH, AKR
Released: 25 May 2016

Explore 5IKQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IKQ contains 91 α-helices and 64 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: 45 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
α-helix	45	1
β-strand	46-50	5	1
β-strand	54-58	5	1
β-strand	64-65	2	2
β-strand	71-72	2	2
α-helix	74-81	8
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-103	7
α-helix	106-121	16
β-strand	130	1	3
β-strand	131	1	4
β-strand	134	1	4
α-helix	139-143	5
β-strand	147	1	5
β-strand	149	1	6
β-strand	150	1	3
α-helix	153-156	4
β-strand	161	1	7
β-strand	164	1	7
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	8
β-strand	189	1	9
β-strand	194	1	10
β-strand	195	1	11
α-helix	196-206	11
β-strand	212	1	12
β-strand	220	1	5
β-strand	221	1	12
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	13
α-helix	251	1
β-strand	252	1	13
α-helix	253	1
β-strand	255-257	3	14
β-strand	260-262	3	14
β-strand	265	1	15
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	15
α-helix	296-319	24
α-helix	325-343	19
α-helix	344-349	6
α-helix	350-353	4
α-helix	363-366	4
β-strand	378	1	6
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	16
β-strand	400-402	3	16
α-helix	404-407	4
α-helix	411-428	18
β-strand	430	1	11
α-helix	431	1
β-strand	432	1	9
α-helix	433	1
β-strand	440	1	8
α-helix	442-444	3
α-helix	445-457	13
α-helix	460-462	3
α-helix	463-469	7
α-helix	473-475	3
α-helix	478-482	5
α-helix	486-495	10
α-helix	498-500	3
α-helix	503-509	7
α-helix	511-513	3
α-helix	520-535	16
α-helix	538-540	3
α-helix	547-550	4
α-helix	553-560	8
α-helix	564-571	8
β-strand	581	1	10

Chain B: 46 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
α-helix	45	1
β-strand	46-50	5	17
β-strand	54-58	5	17
β-strand	64-65	2	18
β-strand	71-72	2	18
α-helix	74-82	9
α-helix	84-85	2
α-helix	86-93	8
α-helix	97-104	8
α-helix	107-122	16
β-strand	132	1	19
β-strand	135	1	19
α-helix	140-144	5
β-strand	148	1	20
β-strand	150	1	19
α-helix	154-157	4
β-strand	162	1	21
β-strand	165	1	21
α-helix	172-174	3
α-helix	175-178	4
α-helix	179-183	5
β-strand	184	1	22
β-strand	190	1	23
β-strand	195	1	24
β-strand	196	1	25
α-helix	197-207	11
β-strand	213	1	26
β-strand	221	1	20
β-strand	222	1	26
α-helix	232-235	4
α-helix	239-245	7
β-strand	246	1	27
α-helix	252	1
β-strand	253	1	27
α-helix	254	1
β-strand	256-258	3	28
β-strand	261-263	3	28
β-strand	266	1	29
α-helix	267-270	4
α-helix	282-284	3
β-strand	286	1	29
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	19
α-helix	380-385	6
α-helix	389-391	3
β-strand	396-398	3	30
β-strand	401-403	3	30
α-helix	405-408	4
α-helix	413-429	17
β-strand	431	1	25
α-helix	432	1
β-strand	433	1	23
α-helix	434	1
β-strand	441	1	22
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
β-strand	513	1	31
α-helix	514	1
β-strand	520	1	31
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	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin G/H synthase 2	A, B	protein	551	Homo sapiens	P35354 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IKQ_1 Prostaglandin G/H synthase 2 (chains A, B)
NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRAL
PPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKT
DHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAE
MIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTS
RLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLP
DTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASI
DQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKP
RPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNV
KGCPFTSFSVP

Ligands and cofactors

ID	Name	Formula	Copies
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	1
JMS	2-[(2,6-dichloro-3-methyl-phenyl)amino]benzoic acid	C14 H11 Cl2 N O2	2
COH	Protoporphyrin IX containing co	C34 H32 Co N4 O4	2
AKR	Acrylic acid	C3 H4 O2	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Substrate-selective Inhibition of Cyclooxygeanse-2 by Fenamic Acid Derivatives Is Dependent on Peroxide Tone. Orlando, B.J., Malkowski, M.G. J Biol Chem (2016) 291:15069-15081. DOI 10.1074/jbc.M116.725713 · PubMed

Other PDB entries of the same protein (UniProt P35354 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F19 2.04 Å, The Crystal Structure of Aspirin Acetylated Human Cyclooxygenase-2
5IKR 2.34 Å, The Structure of Mefenamic Acid Bound to Human Cyclooxygenase-2
5F1A 2.38 Å, The Crystal Structure of Salicylate Bound to Human Cyclooxygenase-2
5IKT 2.45 Å, The Structure of Tolfenamic Acid Bound to Human Cyclooxygenase-2
5IKV 2.51 Å, The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2
5KIR 2.7 Å, The Structure of Vioxx Bound to Human COX-2

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