2zm3

Complex Structure of Insulin-like Growth Factor Receptor and Isoquinolinedione Inhibitor

Method: X-RAY DIFFRACTION Dmax: 116.2 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 981–1286 Fragment:UNP residues 981-1286, IGF-1R Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) 575 (4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.257
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 981–1286 Fragment:UNP residues 981-1286, IGF-1R Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) 575 (4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.257
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 981–1286 Fragment:UNP residues 981-1286, IGF-1R Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) 575 (4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.257
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 981–1286 Fragment:UNP residues 981-1286, IGF-1R Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) 575 (4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.257
5 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 981–1286 Chain B; UniProt 981–1286 Chain C; UniProt 981–1286 Chain D; UniProt 981–1286 Fragment:UNP residues 981-1286, IGF-1R Kinase domain Non-standard monomer:Yes (specific site not provided by mmCIF) 575 (4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinoline-1,3(2H,4H)-dione × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.257

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 88 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 3–308; UniProt 981–1286 Author chain B; PDBConstruct 3–308; UniProt 981–1286 Author chain C; PDBConstruct 3–308; UniProt 981–1286 Author chain D; PDBConstruct 3–308; UniProt 981–1286

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 2zm3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zm3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zm3
Deposition date deposition_date2008-04-10
Structure title titleComplex Structure of Insulin-like Growth Factor Receptor and Isoquinolinedione Inhibitor
Keywords keywords;IGFR, protein-inhibitor complex, tyrosine kinase, ATP-binding, Cleavage on pair of basic residues, Disease mutation, Glycoprotein, Membrane, Nucleotide-binding, Phosphoprotein, Polymorphism, Receptor, Transferase, Transmembrane, Tyrosine-protein kinase ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.26
Radius of gyration Rg (electron density) rg_electron37.47
Forward intensity I(0) i0300270000.00
Molecular weight molecular_weight138840.0 kDa
Excluded volume excluded_volume172920 ų
Envelope volume envelope_volume237440 ų
Hydration-shell volume shell_volume53051 ų
Envelope diameter envelope_diameter114.8
Shell Rg shell_rg43.53
Envelope Rg envelope_rg36.46
Shape Rg shape_rg37.45
Total Rg total_rg37.90
Total atoms total_atoms9700
Residues n_residues1185
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 dmax116.2
Rg (real space) rg_real37.97
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real3.0030e+08
I(0) uncertainty (real space) i0_real_error4.7800e+06
Rg (reciprocal space) rg_reciprocal38.15
I(0) (reciprocal space) i0_reciprocal300300000.0000
Solution quality estimate total_estimate0.8308
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.7
Skewness Skewness skewness-0.038
Kurtosis Kurtosis kurtosis-0.707
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43890000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2zm3a2
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_idd2zm3a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2zm3b2
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_idd2zm3b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2zm3c2
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_idd2zm3c3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2zm3d2
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_idd2zm3d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id2zm3A01
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_id2zm3A02
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_id2zm3B01
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_id2zm3B02
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_id2zm3C01
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_id2zm3C02
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_id2zm3D01
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_id2zm3D02
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)