5m96

Synthesis and biological evaluation of new triazolo and imidazolopyridine RORgt inverse agonists

Method: X-RAY DIFFRACTION Dmax: 77.9 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear receptor ROR-gamma

Homo sapiens

UniProt P51449

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 263–491 Fragment:C-terminal domain, ligand binding domain, UNP residues 263-491 Mutation:C455S Q6Y ~{N}-[8-[[(3~{S})-4-cyclopentylcarbonyl-3-methyl-piperazin-1-yl]methyl]-7-methyl-imidazo[1,2-a]pyridin-6-yl]-2-methyl-pyrimidine-5-carboxamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;1.75M NaFormate, 0.1M PIPES Resolution 1.77 Å R-free 0.208
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 263–491 Fragment:C-terminal domain, ligand binding domain, UNP residues 263-491 Mutation:C455S Q6Y ~{N}-[8-[[(3~{S})-4-cyclopentylcarbonyl-3-methyl-piperazin-1-yl]methyl]-7-methyl-imidazo[1,2-a]pyridin-6-yl]-2-methyl-pyrimidine-5-carboxamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;1.75M NaFormate, 0.1M PIPES Resolution 1.77 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

161 other PDB entries and 266 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RORG_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–230; UniProt 263–491 Author chain B; PDBConstruct 2–230; UniProt 263–491

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5m96

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5m96
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5m96
Deposition date deposition_date2016-10-31
Structure title titleSynthesis and biological evaluation of new triazolo and imidazolopyridine RORgt inverse agonists
Keywords keywordsnuclear hormone receptor, ligand-binding domain, inverse agonist, transcription; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.73
Radius of gyration Rg (electron density) rg_electron23.42
Forward intensity I(0) i047986500.00
Molecular weight molecular_weight53569.0 kDa
Excluded volume excluded_volume67106 ų
Envelope volume envelope_volume81438 ų
Hydration-shell volume shell_volume28514 ų
Envelope diameter envelope_diameter81.6
Shell Rg shell_rg30.95
Envelope Rg envelope_rg23.49
Shape Rg shape_rg23.42
Total Rg total_rg24.30
Total atoms total_atoms3767
Residues n_residues448
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.9
Rg (real space) rg_real24.56
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real4.7990e+07
I(0) uncertainty (real space) i0_real_error6.8550e+05
Rg (reciprocal space) rg_reciprocal24.60
I(0) (reciprocal space) i0_reciprocal47990000.0000
Solution quality estimate total_estimate0.7142
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary76.6
Skewness Skewness skewness0.138
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9939000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.184; Positv: 1.000; Valcen: 0.998; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5m96a_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.0 — automated matches
Domain ID domain_idd5m96b_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id5m96A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5m96B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor

8. Citations (1)

9. Files and Curves (10)