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8t4v

Crystal structure of compound 1 bound to K-Ras(G12D)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GTPase KRas

Homo sapiens

UniProt P01116

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ;4-{(1R,5S)-3-[(7P)-7-(8-ethynylnaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl}-4-oxobutanoic acid ; × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ;4-{(1R,5S)-3-[(7P)-7-(8-ethynylnaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl}-4-oxobutanoic acid ; × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
10jt 10jt 10nu 10nu 10nv 10nv 11qe 3gft 3gft 3gft 3gft 3gft

512 assemblies; showing the first 12

Homodimer
4lrw 4luc 4lv6 4pzy 5v6v 5whd 5whd 6bof 6m9w 6quv 6quw 6qux

22 assemblies; showing the first 12

Homotetramer
8stm

1 assemblies

Other homooligomers
4lyf 4lyh 5oco 5oct 6f76 6fa1 6gog 7acq

8 assemblies

Heteromeric or nucleic-acid complex
1d8d 1d8e 24hr 24hr 24hr 24hr 24hs 24hs 24hs 24hs 24hs 24hs

262 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RASK_HUMAN
Isoform P01116-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 19–187； UniProt 1–169 Author chain B； PDBConstruct 19–187； UniProt 1–169

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t4v
Deposition date deposition_date2023-06-10
Structure title titleCrystal structure of compound 1 bound to K-Ras(G12D)
Keywords keywordsInhibitor, Complex, Covalent, GTPase, ONCOPROTEIN, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8t4v__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8t4v__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8t4v__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）16.55 Å
Rg (electron density)15.14 Å
Total Rg16.28 Å
Atom count1437
Residues170
Excluded volume25325 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8t4v__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8t4v__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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7. Citations (1)