;Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GMPPNP and Covalently Bound to an Adduct of {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2Z)-2-fluoro-3-(pyridin-2-yl)prop-2-enoyl]piperazin-2-yl}acetonitrile ;

条目编号 entry_id	9nzm
沉积日期 deposition_date	2025-04-01
结构标题 title	;Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GMPPNP and Covalently Bound to an Adduct of {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2Z)-2-fluoro-3-(pyridin-2-yl)prop-2-enoyl]piperazin-2-yl}acetonitrile ;
关键词 keywords	KRAS, GTPASE, INHIBITOR, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	22.96 Å
回转半径 Rg (电子) rg_electron	22.30 Å
零角强度 I(0) i0	26829800.00
分子量 molecular_weight	38504.0 kDa
排除体积 excluded_volume	47683 ų
包络体积 envelope_volume	55896 ų
水化壳体积 shell_volume	21642 ų
包络直径 envelope_diameter	82.9 Å
壳层 Rg shell_rg	28.19 Å
包络 Rg envelope_rg	22.62 Å
形状 Rg shape_rg	22.31 Å
总 Rg total_rg	23.02 Å
总原子数 total_atoms	5315
残基数 n_residues	321
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å−1
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/ų
壳层衬度 contrast_shell	0.0300 e/ų
CRYSOL 版本 crysol_version	4.1.3

最大尺寸 Dmax dmax	80.6 Å
Rg (实空间) rg_real	23.01 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	2.6830e+07
I(0) 误差 (实空间) i0_real_error	3.6180e+05
Rg (倒空间) rg_reciprocal	23.00 Å
I(0) (倒空间) i0_reciprocal	26830000.0000
解质量估计 total_estimate	0.8514
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.0 Å
偏度 Skewness skewness	0.452
峰度 Kurtosis kurtosis	-0.204
角度范围 angular_range	— – 0.3450 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4223000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.991

晶胞参数 Unit Cell

晶胞边长 a length_a	111.788 Å
晶胞边长 b length_b	70.420 Å
晶胞边长 c length_c	62.783 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.07 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

对称性 Symmetry

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

精修参数 Refinement

分辨率 resolution	1.586 Å
最低分辨率 resolution_low	18.140 Å
R 因子 r_factor	0.2103
R_work r_work	0.2093
R_free r_free	0.2293

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/nz/9nzm/pr_distribution.json
• pr_output /app/data/pr_computation/nz/9nzm/9nzm.pr.out
• pr_plot /app/data/visualization/pr_computation/nz/9nzm/9nzm_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/nz/9nzm/9nzm.dat
• saxs_fit /app/data/saxs_computation/nz/9nzm/9nzm.fit
• saxs_log /app/data/saxs_computation/nz/9nzm/9nzm.log
• saxs_plot /app/data/visualization/saxs_computation/nz/9nzm/9nzm_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/nz/9nzm/9nzm.fit
pddf	/app/data/pr_computation/nz/9nzm/9nzm.pr.out
profile	/app/data/saxs_computation/nz/9nzm/9nzm.dat