9LLI: D1R

Cryo-EM structure of D1R in complex with de novo designed GEM targeting TM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7. Determined by electron microscopy at 3.0 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,466
Mol. weight: 88.92 kDa
Ligands: A1EKL
Released: 4 Mar 2026

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

Secondary structure: helices and β-sheets

9LLI contains 31 α-helices and 0 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 O: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-30	29
α-helix	34-67	34

Chain P: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-35	29
α-helix	40-42	3
α-helix	43-70	28

Chain Q: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-43	30
α-helix	46-77	32

Chain R: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	19-22	4
α-helix	25-50	26
α-helix	52-55	4
α-helix	58-60	3
α-helix	61-72	12
α-helix	73-77	5
α-helix	78-87	10
α-helix	93-95	3
α-helix	96-126	31
α-helix	128-134	7
α-helix	137-159	23
α-helix	193-199	7
α-helix	200-204	5
α-helix	205-1023	39
α-helix	1028-1046	19
α-helix	1067-1086	20
α-helix	1089-1104	16
α-helix	1107-1114	8
α-helix	1115-1119	5
α-helix	1120-294	26
α-helix	311-321	11
α-helix	323-330	8
α-helix	331-333	3
α-helix	335-345	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
D(1A) dopamine receptor	R	protein	519	Homo sapiens	P21728 (AlphaFold model)
De novo designed GPCR exoframe modulator targeting TM1/2/4	O	protein	97	synthetic construct
De novo designed GPCR exoframe modulator targeting TM3/4/5	P	protein	77	Homo sapiens
De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7	Q	protein	95	Homo sapiens

Sequence of entity 1 (R), FASTA

>9LLI_1 D(1A) dopamine receptor (chains R)
RTLNTSAMDGTGLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTNF
FVISLAVSDLLVAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASILNLCVISVDR
YWAISSPFRYERKMTPKAAFILISVAWTLSVLISFIPVQLSNHKAKPTSPSDGNATSLAE
TIDNCDSSLSRTYAISSSVISFYIPVAIMIVTYTRIYRILKKELDALNDNWETLNDNLKV
IEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDAL
KLANEGKVKEAQAAAEQLKTTRDAILKPFIEELKELKGKPFLIDAVIMGVFVCCWLPFFI
LNCILPFCGSGETQPFCIDSNTFDVFVWFGWANSSLNPIIYAFNADFRKAFSTLLGCYRL
CPATNNAIETVSINNNGAAMFSSHHEPRGSISKECNLVYLIPHAVGSSEDLKKEEAAGIA
RPLEKLSPALSVILDYDTDVSLEKIQPITQNGQHPTGGS

Sequence of entity 2 (O), FASTA

>9LLI_2 De novo designed GPCR exoframe modulator targeting TM1/2/4 (chains O)
DYKDDDDKEFLEVLFQGPMLLIIGTIITLVSSIIFLISFFRFMRKWIRGLTRRDVRRFLV
VLLVFFLLFLISLLLYVLFLVLYFLSLGKIDPKTGSA

Sequence of entity 3 (P), FASTA

>9LLI_3 De novo designed GPCR exoframe modulator targeting TM3/4/5 (chains P)
GPPLPLSKIVILLIILLILSIIFLLLLYLLIKYFKSFNEPIPPMLKVFLIYCVLSLIWVI
IYTIIEVLELLLRPPPG

Sequence of entity 4 (Q), FASTA

>9LLI_4 De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7 (chains Q)
PSPVPPPPPPLPIWKILLIIGTILYIVVFLYISIFLYRLLKTFVPKEERKKWFKFLGILF
LIFLILLIYFVVYVIRVLFPPPPPPSPGPPPPPPP

Ligands and cofactors

ID	Name	Formula	Copies
A1EKL	Flupentixol	C23 H25 F3 N2 O S	1

Primary citation

GPCR exoframe modulators. Cheng, S., Guo, J., Zhou, Y. et al. To be published.

Other PDB entries of the same protein (UniProt P21728 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
9WG0 2.59 Å, D1R-Gs in complexed with SKF81297/LY3154207/BMSA1/UNC10062
9LLJ 2.61 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targetingTM1/2/4 and…
9LLF 2.64 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM3/4/5
9WEU 2.65 Å, D1R-Gs in complexed with SKF81297/LY3154207/BMSA1
9I54 2.72 Å, Dopamine 1 receptor:GaS complex bound to 24
9LLH 2.73 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed agonist-positive allosteric…
9LLG 2.77 Å, Cryo-EM structure of D1R in complex with de novo designed negative allosteric GEM…
9I52 2.8 Å, Dopamine 1 receptor:GaS complex bound to 19B
7JVP 2.9 Å, Cryo-EM structure of SKF-83959-bound dopamine receptor 1 in complex with Gs protein
9LLE 2.9 Å, Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM1/2/4
9LWC 2.9 Å, Cryo-EM structure of epinephrine bound dopamine receptor 1…

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