5KIR: Vioxx

The Structure of Vioxx Bound to Human COX-2. Determined by X-ray diffraction at 2.7 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,344
Mol. weight: 131 kDa
Ligands: RCX, COH, NAG, PO4
Released: 28 Sept 2016

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

Secondary structure: helices and β-sheets

5KIR contains 90 α-helices and 68 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
α-helix	35-38	4
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	86-93	8
α-helix	97-104	8
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
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	255-257	3	12
β-strand	260-262	3	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
β-strand	462	1	15
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
β-strand	502	1	15
α-helix	503-509	7
α-helix	511	1
β-strand	512	1	16
α-helix	513	1
β-strand	519	1	16
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: 46 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
α-helix	45	1
β-strand	46-49	4	17
β-strand	55-58	4	17
β-strand	64-65	2	18
β-strand	71-72	2	18
α-helix	73	1
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	1	19
β-strand	131	1	20
β-strand	134	1	20
α-helix	139-143	5
β-strand	147	1	21
β-strand	149	1	22
β-strand	150	1	19
α-helix	153-156	4
β-strand	161	1	23
β-strand	164	1	23
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	24
β-strand	189	1	25
β-strand	194	1	26
β-strand	195	1	27
α-helix	196-206	11
β-strand	212	1	28
β-strand	220	1	21
β-strand	221	1	28
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	29
α-helix	251	1
β-strand	252	1	29
α-helix	253	1
β-strand	255-257	3	30
β-strand	260-262	3	30
β-strand	265	1	31
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	31
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	22
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	32
β-strand	400-402	3	32
α-helix	404-407	4
α-helix	411-428	18
β-strand	430	1	27
α-helix	431	1
β-strand	432	1	25
α-helix	433	1
β-strand	440	1	24
α-helix	442-444	3
α-helix	445-457	13
α-helix	463-469	7
α-helix	473-475	3
α-helix	478-482	5
α-helix	486-494	9
α-helix	498-500	3
α-helix	503-509	7
α-helix	511	1
β-strand	512	1	33
α-helix	513	1
β-strand	519	1	33
α-helix	520-535	16
α-helix	538-540	3
α-helix	547-550	4
α-helix	553-561	9
α-helix	564-571	8
β-strand	581	1	26

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

>5KIR_1 Prostaglandin G/H synthase 2 (chains A, B)
NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRAL
PPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKT
DHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAE
MIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTS
RLILIGETIKIVIEDYVNHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLP
DTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASI
DQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKP
RPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNV
KGCPFTSFSVP

Ligands and cofactors

ID	Name	Formula	Copies
RCX	Rofecoxib	C17 H14 O4 S	2
COH	Protoporphyrin IX containing co	C34 H32 Co N4 O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PO4	Phosphate ion	O4 P	6

Water and common crystallization additives (NH4, GOL) are not listed.

Primary citation

Crystal structure of rofecoxib bound to human cyclooxygenase-2. Orlando, B.J., Malkowski, M.G. Acta Crystallogr F Struct Biol Commun (2016) 72:772-776. DOI 10.1107/S2053230X16014230 · 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
5IKQ 2.41 Å, The Structure of Meclofenamic Acid 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

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5KIR is part of these collections:

Drugs bound to their targets

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