3LN0: Compound 5c-S bound at the active site of COX-2

Structure of compound 5c-S bound at the active site of COX-2. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Oct 2010.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 19,611
Mol. weight: 277.91 kDa
Ligands: BOG, 52B, NAG, HEM
Released: 27 Oct 2010

Explore 3LN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3LN0 contains 170 α-helices and 130 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: 43 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	1
β-strand	40-43	4	1
β-strand	49-50	2	2
β-strand	56-57	2	2
α-helix	59-66	8
α-helix	71-78	8
α-helix	82-88	7
α-helix	92-107	16
β-strand	116-117	2	3
β-strand	120	1	3
α-helix	125-129	5
β-strand	133	1	4
β-strand	135-136	2	3
α-helix	139-142	4
β-strand	147	1	5
β-strand	150	1	5
α-helix	157-159	3
α-helix	160-163	4
α-helix	164-168	5
β-strand	169	1	6
β-strand	175	1	7
β-strand	180	1	8
β-strand	181	1	9
α-helix	182-192	11
β-strand	198	1	10
β-strand	206	1	4
β-strand	207	1	10
α-helix	217-220	4
α-helix	224-230	7
β-strand	231	1	11
α-helix	237	1
β-strand	238	1	11
α-helix	239	1
β-strand	241-243	3	12
β-strand	246-248	3	12
β-strand	251	1	13
α-helix	252-255	4
α-helix	267-269	3
β-strand	271	1	13
α-helix	278-280	3
α-helix	282-305	24
α-helix	311-329	19
α-helix	330-335	6
α-helix	336-339	4
α-helix	349-352	4
β-strand	364	1	3
α-helix	365-370	6
α-helix	374-376	3
β-strand	381-383	3	14
β-strand	386-388	3	14
α-helix	390-393	4
α-helix	398-414	17
β-strand	416	1	9
α-helix	417	1
β-strand	418	1	7
α-helix	419	1
β-strand	426	1	6
α-helix	428-430	3
α-helix	431-443	13
α-helix	446-448	3
α-helix	449-455	7
α-helix	459-461	3
α-helix	464-468	5
α-helix	472-481	10
α-helix	484-486	3
α-helix	489-495	7
α-helix	497-498	2
α-helix	506-521	16
α-helix	524-526	3
α-helix	533-536	4
α-helix	539-546	8
α-helix	550-557	8
β-strand	567	1	8

Chain B: 43 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	15
β-strand	40-43	4	15
β-strand	49-50	2	16
β-strand	56-57	2	16
α-helix	59-66	8
α-helix	71-78	8
α-helix	82-88	7
α-helix	92-107	16
β-strand	116	1	17
β-strand	117	1	18
β-strand	120	1	18
α-helix	125-129	5
β-strand	133	1	19
β-strand	135	1	20
β-strand	136	1	17
α-helix	139-142	4
β-strand	147	1	21
β-strand	150	1	21
α-helix	157-159	3
α-helix	160-163	4
α-helix	164-168	5
β-strand	169	1	22
β-strand	175	1	23
β-strand	180	1	24
β-strand	181	1	25
α-helix	182-192	11
β-strand	198	1	26
β-strand	206	1	19
β-strand	207	1	26
α-helix	217-220	4
α-helix	224-230	7
β-strand	231	1	27
α-helix	237	1
β-strand	238	1	27
α-helix	239	1
β-strand	241-243	3	28
β-strand	246-248	3	28
β-strand	251	1	29
α-helix	252-255	4
α-helix	267-269	3
β-strand	271	1	29
α-helix	278-280	3
α-helix	282-305	24
α-helix	311-329	19
α-helix	330-335	6
α-helix	336-339	4
α-helix	349-352	4
β-strand	364	1	20
α-helix	365-370	6
α-helix	374-376	3
β-strand	381-383	3	30
β-strand	386-388	3	30
α-helix	390-393	4
α-helix	397-414	18
β-strand	416	1	25
α-helix	417	1
β-strand	418	1	23
α-helix	419	1
β-strand	426	1	22
α-helix	428-430	3
α-helix	431-443	13
α-helix	446-448	3
α-helix	449-455	7
α-helix	459-461	3
α-helix	464-468	5
α-helix	472-481	10
α-helix	484-486	3
α-helix	489-495	7
α-helix	497	1
β-strand	498	1	31
β-strand	505	1	31
α-helix	506-521	16
α-helix	524-526	3
α-helix	533-536	4
α-helix	539-546	8
α-helix	550-557	8
β-strand	567	1	24

Chain C: 42 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	32
β-strand	40-43	4	32
β-strand	49-50	2	33
β-strand	56-57	2	33
α-helix	59-66	8
α-helix	71-78	8
α-helix	82-88	7
α-helix	92-107	16
β-strand	116	1	34
β-strand	117	1	35
β-strand	120	1	35
α-helix	125-129	5
β-strand	133	1	36
β-strand	135	1	37
β-strand	136	1	34
α-helix	139-142	4
β-strand	147	1	38
β-strand	150	1	38
α-helix	157-159	3
α-helix	160-163	4
α-helix	164-168	5
β-strand	169	1	39
β-strand	175	1	40
β-strand	180	1	41
β-strand	181	1	42
α-helix	182-192	11
β-strand	198	1	43
β-strand	206	1	36
β-strand	207	1	43
α-helix	217-220	4
α-helix	224-230	7
β-strand	231	1	44
α-helix	237	1
β-strand	238	1	44
α-helix	239	1
β-strand	241-243	3	45
β-strand	246-248	3	45
β-strand	251	1	46
α-helix	252-255	4
α-helix	267-269	3
β-strand	271	1	46
α-helix	282-305	24
α-helix	311-329	19
α-helix	330-335	6
α-helix	336-339	4
α-helix	349-352	4
β-strand	364	1	37
α-helix	365-370	6
α-helix	374-376	3
β-strand	381-383	3	47
β-strand	386-388	3	47
α-helix	390-393	4
α-helix	398-414	17
β-strand	416	1	42
α-helix	417	1
β-strand	418	1	40
α-helix	419	1
β-strand	426	1	39
α-helix	428-430	3
α-helix	431-443	13
α-helix	446-448	3
α-helix	449-455	7
α-helix	459-461	3
α-helix	464-468	5
α-helix	472-481	10
α-helix	484-486	3
α-helix	489-495	7
α-helix	497-498	2
α-helix	506-521	16
α-helix	524-526	3
α-helix	533-536	4
α-helix	539-546	8
α-helix	550-557	8
β-strand	567	1	41

Chain D: 42 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	48
β-strand	40-43	4	48
β-strand	49-50	2	49
β-strand	56-57	2	49
α-helix	59-66	8
α-helix	71-78	8
α-helix	82-88	7
α-helix	92-107	16
β-strand	116	1	50
β-strand	117	1	51
β-strand	120	1	51
α-helix	125-129	5
β-strand	133	1	52
β-strand	135	1	53
β-strand	136	1	50
α-helix	139-142	4
β-strand	147	1	54
β-strand	150	1	54
α-helix	157-159	3
α-helix	160-163	4
α-helix	164-168	5
β-strand	169	1	55
β-strand	175	1	56
β-strand	180	1	57
β-strand	181	1	58
α-helix	182-192	11
β-strand	198	1	59
β-strand	206	1	52
β-strand	207	1	59
α-helix	217-220	4
α-helix	224-230	7
β-strand	231	1	60
α-helix	237	1
β-strand	238	1	60
α-helix	239	1
β-strand	241-243	3	61
β-strand	246-248	3	61
β-strand	251	1	62
α-helix	252-255	4
α-helix	267-269	3
β-strand	271	1	62
α-helix	278-280	3
α-helix	282-305	24
α-helix	311-329	19
α-helix	330-335	6
α-helix	336-339	4
α-helix	349-352	4
β-strand	364	1	53
α-helix	365-370	6
α-helix	374-376	3
β-strand	381-383	3	63
β-strand	386-388	3	63
α-helix	390-393	4
α-helix	397-414	18
β-strand	416	1	58
α-helix	417	1
β-strand	418	1	56
α-helix	419	1
β-strand	426	1	55
α-helix	428-430	3
α-helix	431-443	13
α-helix	449-455	7
α-helix	459-461	3
α-helix	464-468	5
α-helix	472-481	10
α-helix	484-486	3
α-helix	489-495	7
α-helix	497	1
β-strand	498	1	64
β-strand	505	1	64
α-helix	506-521	16
α-helix	524-526	3
α-helix	533-536	4
α-helix	539-546	8
α-helix	550-557	8
β-strand	567	1	57

Molecules and chains

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

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

>3LN0_1 Prostaglandin G/H synthase 2 (chains A, B, C, D)
ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYI
LTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRA
LPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFK
TDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV
EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQT
SRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLL
PDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKAS
IDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK
PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNN
VKGCPFTSFNVQDPQPTKTATINASASHSRLDDINPTVLIKRRSTEL

Ligands and cofactors

ID	Name	Formula	Copies
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	2
52B	(2S)-6,8-dichloro-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid	C11 H5 Cl2 F3 O3	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4

Primary citation

The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life. Wang, J.L., Limburg, D., Graneto, M.J. et al. Bioorg Med Chem Lett (2010) 20:7159-7163. DOI 10.1016/j.bmcl.2010.07.054 · 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)

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