9KT7: HCA2-Gi complex with MK6892

Cryo-EM structure of HCA2-Gi complex with MK6892. Determined by electron microscopy at 2.8 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,094
Mol. weight: 156.66 kDa
Ligands: FI7
Released: 10 Dec 2025

Explore 9KT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KT7 contains 38 α-helices and 66 β-strands across 5 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	3
α-helix	46-53	8
β-strand	185-191	7	3
β-strand	194-200	7	3
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-225	6	3
α-helix	227-229	3
β-strand	233	1	4
β-strand	241	1	4
α-helix	242-254	13
β-strand	263-268	6	3
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	3
α-helix	330-347	18

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-43	6
β-strand	47-51	5	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
β-strand	134-139	6	7
β-strand	146-151	6	8
β-strand	156-161	6	8
β-strand	166-170	5	8
β-strand	176-180	5	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	207-212	6	9
β-strand	218-223	6	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	259-264	6	10
α-helix	272	1
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	26-27	2
α-helix	30-43	14
α-helix	53-55	3

Chain E: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
α-helix	53-55	3
β-strand	58-60	3	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	110-111	2	13
β-strand	113	1	12
β-strand	115-119	5	13
β-strand	140-141	2	14
β-strand	146-148	3	15
β-strand	155-161	7	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	15
β-strand	186-190	5	15
β-strand	194-195	2	15
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	226-231	6	15
α-helix	237	1
β-strand	239	1	15
α-helix	240-242	3
β-strand	243-246	4	15

Chain R: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	1
β-strand	17-19	3	1
α-helix	25-50	26
α-helix	51-55	5
α-helix	61-77	17
α-helix	80-88	9
α-helix	98-130	33
α-helix	135-137	3
α-helix	141-159	19
α-helix	160-164	5
β-strand	169-171	3	2
β-strand	174-176	3	2
β-strand	182-183	2	1
α-helix	188-217	30
α-helix	226-260	35
α-helix	267-279	13
α-helix	280-282	3
α-helix	283-290	8
α-helix	291-296	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hydroxycarboxylic acid receptor 2	R	protein	363	Homo sapiens	Q8TDS4 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFV	E	protein	267	Homo sapiens

Sequence of entity 1 (R), FASTA

>9KT7_1 Hydroxycarboxylic acid receptor 2 (chains R)
MNRHHLQDHFLEIDKKNCCVFRDDFIVKVLPPVLGLEFIFGLLGNGLALWIFCFHLKSWK
SSRIFLFNLAVADFLLIICLPFLMDNYVRRWDWKFGDIPCRLMLFMLAMNRQGSIIFLTV
VAVDRYFRVVHPHHALNKISNRTAAIISCLLWGITIGLTVHLLKKKMPIQNGGANLCSSF
SICHTFQWHEAMFLLEFFLPLGIILFCSARIIWSLRQRQMDRHAKIKRAITFIMVVAIVF
VICFLPSVVVRIRIFWLLHTSGTQNCEVYRSVDLAFFITLSFTYMNSMLDPVVYYFSSPS
FPNFFSTLINRCLQRKMTGEPDNNRSTSVELTGDPNKTRGAPEALMANSGEPWSPSYLGP
TSP

Sequence of entity 2 (A), FASTA

>9KT7_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9KT7_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>9KT7_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>9KT7_5 scFV (chains E)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
FI7	2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]a…	C19 H22 N4 O5	1

Primary citation

Insights into the Activation Mechanism of HCA1, HCA2, and HCA3. Wang, J., Qian, Y., Han, Z. et al. J Med Chem (2025) 68:4527-4539. DOI 10.1021/acs.jmedchem.4c02567 · PubMed

Other PDB entries of the same protein (UniProt Q8TDS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8J6P 2.55 Å, Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex
8J6Q 2.6 Å, Cryo-EM structure of the 3-HB and compound 9n-bound human HCAR2-Gi1 complex
8JZ7 2.6 Å, Cryo-EM structure of MK-6892-bound HCAR2 in complex with Gi protein
9IZC 2.68 Å, Cryo-EM structure of human HCAR2-Gi complex with MK1903
8IJA 2.69 Å, Cryo-EM structure of human HCAR2-Gi complex with niacin
7ZL9 2.7 Å, Crystal structure of human GPCR Niacin receptor (HCA2)
7ZLY 2.7 Å, Crystal structure of human GPCR Niacin receptor (HCA2) expressed from Spodoptera…
9JKY 2.72 Å, acifran-HCAR2-Gi complex
9KT8 2.73 Å, Cryo-EM structure of HCA2-Gi complex with acifran
8J6R 2.76 Å, Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex
8I7V 2.77 Å, Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 in complex…
8J6J 2.8 Å, Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound with…

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