5hzn

Structure of NVP-AEW541 in complex with IGF-1R kinase

Method: X-RAY DIFFRACTION Dmax: 161.5 Å Quality: GOOD

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

Insulin-like growth factor 1 receptor

Homo sapiens

UniProt P08069

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 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 983–1286 Not recorded 66A 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;293 K;25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL Resolution 2.20 Å R-free 0.218

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.

44 other PDB entries and 85 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGF1R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–304; UniProt 983–1286 Author chain B; PDBConstruct 1–304; UniProt 983–1286 Author chain C; PDBConstruct 1–304; UniProt 983–1286 Author chain D; PDBConstruct 1–304; UniProt 983–1286 Author chain E; PDBConstruct 1–304; UniProt 983–1286 Author chain F; PDBConstruct 1–304; UniProt 983–1286 Author chain G; PDBConstruct 1–304; UniProt 983–1286 Author chain H; PDBConstruct 1–304; UniProt 983–1286

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 5hzn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5hzn
Deposition date deposition_date2016-02-02
Structure title titleStructure of NVP-AEW541 in complex with IGF-1R kinase
Keywords keywordsInhibitor, Kinase, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier48.71
Radius of gyration Rg (electron density) rg_electron48.79
Forward intensity I(0) i01102450000.00
Molecular weight molecular_weight276350.0 kDa
Excluded volume excluded_volume345630 ų
Envelope volume envelope_volume478450 ų
Hydration-shell volume shell_volume81897 ų
Envelope diameter envelope_diameter162.2
Shell Rg shell_rg52.38
Envelope Rg envelope_rg47.90
Shape Rg shape_rg48.79
Total Rg total_rg48.92
Total atoms total_atoms19355
Residues n_residues2383
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 dmax161.5
Rg (real space) rg_real48.82
Rg uncertainty (real space) rg_real_error1.36
I(0) (real space) i0_real1.1020e+09
I(0) uncertainty (real space) i0_real_error2.2060e+07
Rg (reciprocal space) rg_reciprocal48.71
I(0) (reciprocal space) i0_reciprocal1102000000.0000
Solution quality estimate total_estimate0.8715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.5
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.561
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha108600000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.760

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5hzna_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hznb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hznc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hznd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hzne_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hznf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hzng_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5hznh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (16 domains)

Domain ID domain_id5hznA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5hznH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5hznH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)