5sy2

Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors

Method: X-RAY DIFFRACTION Dmax: 87.7 Å Quality: REASONABLE

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

Renin

Homo sapiens

UniProt P00797

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 67–406 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 74V N-ethyl-4-{[(furan-2-yl)methyl]amino}-2-methyl-N-[(3S)-piperidin-3-yl]pyrimidine-5-carboxamide × 1 PGE TRIETHYLENE GLYCOL × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;293 K;23% PEG600, 0.06M citrate, 0.04M citric acid Resolution 2.25 Å R-free 0.221
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 67–406 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 74V N-ethyl-4-{[(furan-2-yl)methyl]amino}-2-methyl-N-[(3S)-piperidin-3-yl]pyrimidine-5-carboxamide × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;293 K;23% PEG600, 0.06M citrate, 0.04M citric acid Resolution 2.25 Å R-free 0.221
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 67–406 Chain B; UniProt 67–406 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 74V N-ethyl-4-{[(furan-2-yl)methyl]amino}-2-methyl-N-[(3S)-piperidin-3-yl]pyrimidine-5-carboxamide × 6 PGE TRIETHYLENE GLYCOL × 3 DMS DIMETHYL SULFOXIDE × 6 1PE PENTAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;293 K;23% PEG600, 0.06M citrate, 0.04M citric acid Resolution 2.25 Å R-free 0.221

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.

90 other PDB entries and 227 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RENI_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–340; UniProt 67–406 Author chain B; PDBConstruct 1–340; UniProt 67–406

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 5sy2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5sy2
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5sy2
Deposition date deposition_date2016-08-10
Structure title titleStructure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors
Keywords keywordsprotein-ligand complex, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.09
Radius of gyration Rg (electron density) rg_electron27.23
Forward intensity I(0) i085292100.00
Molecular weight molecular_weight73638.0 kDa
Excluded volume excluded_volume92558 ų
Envelope volume envelope_volume112010 ų
Hydration-shell volume shell_volume34203 ų
Envelope diameter envelope_diameter93.9
Shell Rg shell_rg34.68
Envelope Rg envelope_rg27.27
Shape Rg shape_rg27.18
Total Rg total_rg28.17
Total atoms total_atoms5183
Residues n_residues665
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 dmax87.7
Rg (real space) rg_real28.05
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real8.5290e+07
I(0) uncertainty (real space) i0_real_error9.7830e+05
Rg (reciprocal space) rg_reciprocal28.07
I(0) (reciprocal space) i0_reciprocal85290000.0000
Solution quality estimate total_estimate0.7188
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.3
Skewness Skewness skewness0.311
Kurtosis Kurtosis kurtosis-0.456
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19510000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.999; Smooth: 0.810

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5sy2a_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.2 — Pepsin-like
Domain ID domain_idd5sy2b_
Class classb — All beta proteins
Fold Fold foldb.50 — Acid proteases
Superfamily Superfamily superfamilyb.50.1 — Acid proteases
Family Family familyb.50.1.2 — Pepsin-like

CATH v4.4 (4 domains)

Domain ID domain_id5sy2A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id5sy2A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id5sy2B01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id5sy2B02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases

8. Citations (1)

9. Files and Curves (10)