5CGD: PDB entry 5CGD

Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile - (HTL14242). Determined by X-ray diffraction at 2.6 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,345
Mol. weight: 51.24 kDa
Ligands: OLA, 51E
Released: 12 Aug 2015

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

Secondary structure: helices and β-sheets

5CGD contains 20 α-helices and 9 β-strands across 1 chain. 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: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	569-575	7
α-helix	579-603	25
α-helix	608-611	4
α-helix	615-630	16
α-helix	632-635	4
β-strand	636	1	1
α-helix	641-1010	47
β-strand	1016	1	2
β-strand	1018-1019	2	3
β-strand	1025-1027	3	3
β-strand	1031-1032	2	3
α-helix	1039-1050	12
β-strand	1057	1	2
α-helix	1060-1079	20
α-helix	1085-1090	6
α-helix	1093-1106	14
α-helix	1108-1111	4
α-helix	1115-1122	8
α-helix	1126-1133	8
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	690-714	25
β-strand	719	1	4
β-strand	730	1	1
β-strand	733	1	4
α-helix	737-760	24
α-helix	766-792	27
α-helix	798-817	20
α-helix	819-827	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5	A	protein	444	Homo sapiens, Enterobacteria phage T4	P00720, P41594 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5CGD_1 Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5 (chains A)
AASPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSRELCYIILAGI
CLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTYRAARILAMSKKNIFEMLR
IDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFN
QDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDE
AAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKICTKKPRFMSACAQLVIAFILICIQL
GIIVALFIMEPPDIMHDYPSIREVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVP
ANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVYII
LAKPERNVRSAAAAHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	4
51E	3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile	C16 H8 Cl F N4	1

Primary citation

Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile). Christopher, J.A., Aves, S.J., Bennett, K.A. et al. J Med Chem (2015) 58:6653-6664. DOI 10.1021/acs.jmedchem.5b00892 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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