3NTB: 6-methylthio naproxen analog

Structure of 6-methylthio naproxen analog bound to mCOX-2. Determined by X-ray diffraction at 2.27 Å resolution. Released 1 Sept 2010.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Mus musculus
Chains: 4
Atoms: 19,636
Mol. weight: 278.82 kDa
Ligands: HEM, NAG, BOG, T1N
Released: 1 Sept 2010

Explore 3NTB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NTB contains 184 α-helices and 128 β-strands across 4 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: 46 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	1
β-strand	55-58	4	1
β-strand	64-65	2	2
β-strand	71-72	2	2
α-helix	73	1
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-94	9
α-helix	97-103	7
α-helix	106-121	16
β-strand	130-131	2	3
β-strand	134	1	3
α-helix	139-143	5
β-strand	147	1	4
α-helix	148	1
β-strand	149-150	2	3
α-helix	153-156	4
β-strand	161	1	5
β-strand	164	1	5
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	6
β-strand	189	1	7
β-strand	194	1	8
β-strand	195	1	9
α-helix	196-206	11
β-strand	212	1	10
β-strand	220	1	4
β-strand	221	1	10
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	11
α-helix	251	1
β-strand	252	1	11
α-helix	253	1
β-strand	255-256	2	12
β-strand	261-262	2	12
β-strand	265	1	13
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	13
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	3
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	14
β-strand	400-402	3	14
α-helix	404-407	4
α-helix	412-428	17
β-strand	430	1	9
α-helix	431	1
β-strand	432	1	7
α-helix	433	1
β-strand	440	1	6
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	1
β-strand	512	1	15
α-helix	513	1
β-strand	519	1	15
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	8

Chain B: 47 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	16
β-strand	55-58	4	16
β-strand	64-65	2	17
β-strand	71-72	2	17
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-103	7
α-helix	106-121	16
β-strand	130-131	2	18
β-strand	134	1	18
α-helix	139-143	5
β-strand	147	1	19
α-helix	148	1
β-strand	149-150	2	18
α-helix	153-156	4
β-strand	161	1	20
β-strand	164	1	20
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	21
β-strand	189	1	22
β-strand	194	1	23
β-strand	195	1	24
α-helix	196-206	11
β-strand	212	1	25
β-strand	220	1	19
β-strand	221	1	25
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	26
α-helix	251	1
β-strand	252	1	26
α-helix	253	1
β-strand	255-257	3	27
β-strand	260-262	3	27
α-helix	263-264	2
β-strand	265	1	28
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	28
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	18
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	29
β-strand	400-402	3	29
α-helix	404-407	4
α-helix	412-417	6
α-helix	419-428	10
β-strand	430	1	24
α-helix	431	1
β-strand	432	1	22
α-helix	433	1
β-strand	440	1	21
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	1
β-strand	512	1	30
α-helix	513	1
β-strand	519	1	30
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	23

Chain C: 46 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	31
β-strand	55-58	4	31
β-strand	64-65	2	32
β-strand	71-72	2	32
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-104	8
α-helix	106-121	16
β-strand	130-131	2	33
β-strand	134	1	33
α-helix	139-143	5
β-strand	147	1	34
β-strand	149-150	2	33
α-helix	153-156	4
β-strand	161	1	35
β-strand	164	1	35
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	36
β-strand	189	1	37
β-strand	194	1	38
β-strand	195	1	39
α-helix	196-206	11
β-strand	212	1	40
β-strand	220	1	34
β-strand	221	1	40
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	41
α-helix	251	1
β-strand	252	1	41
α-helix	253	1
β-strand	255-257	3	42
β-strand	260-262	3	42
α-helix	263-264	2
β-strand	265	1	43
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	43
α-helix	292-294	3
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	33
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	44
β-strand	400-402	3	44
α-helix	404-407	4
α-helix	412-417	6
α-helix	419-428	10
β-strand	430	1	39
α-helix	431	1
β-strand	432	1	37
α-helix	433	1
β-strand	440	1	36
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	38

Chain D: 45 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
β-strand	46-49	4	45
β-strand	55-58	4	45
β-strand	64-65	2	46
β-strand	71-72	2	46
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-94	9
α-helix	97-104	8
α-helix	106-121	16
β-strand	130	1	47
β-strand	131	1	48
β-strand	134	1	48
α-helix	139-143	5
β-strand	147	1	49
α-helix	148	1
β-strand	149	1	50
β-strand	150	1	47
α-helix	153-156	4
β-strand	161	1	51
β-strand	164	1	51
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	52
β-strand	189	1	53
β-strand	194	1	54
β-strand	195	1	55
α-helix	196-206	11
β-strand	212	1	56
β-strand	220	1	49
β-strand	221	1	56
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	57
α-helix	251	1
β-strand	252	1	57
α-helix	253	1
β-strand	255-257	3	58
β-strand	260-262	3	58
β-strand	265	1	59
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	59
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	50
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	60
β-strand	400-402	3	60
α-helix	404-407	4
α-helix	412-417	6
α-helix	419-428	10
β-strand	430	1	55
α-helix	431	1
β-strand	432	1	53
α-helix	433	1
β-strand	440	1	52
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
β-strand	512	1	61
β-strand	519	1	61
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	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin-endoperoxide synthase 2	A, B, C, D	protein	587	Mus musculus	Q05769 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3NTB_1 Prostaglandin-endoperoxide synthase 2 (chains A, B, C, D)
ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYI
LTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRA
LPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFK
TDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV
EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQT
SRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLL
PDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKAS
IDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK
PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNN
VKGCPFTSFNVQDPQPTKTATINASASHSRLDDINPTVLIKRRSTEL

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	6
T1N	(2S)-2-[6-(methylsulfanyl)naphthalen-2-yl]propanoic acid	C14 H14 O2 S	4

Primary citation

Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen. Duggan, K.C., Walters, M.J., Musee, J. et al. J Biol Chem (2010) 285:34950-34959. DOI 10.1074/jbc.M110.162982 · 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.
4PH9 1.81 Å, The structure of Ibuprofen bound to cyclooxygenase-2
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)

Browse structure collections

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