8pqc

c-KIT kinase domain in complex with avapritinib derivative 9

Method: X-RAY DIFFRACTION D_max: 113.0 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8pqc
沉积日期 deposition_date	2023-07-11
结构标题 title	c-KIT kinase domain in complex with avapritinib derivative 9
关键词 keywords	;c-KIT, protein kinase, avapritinib, inhibitor, tyrosine kinase, transmembrane receptor, stem cell factor, stem cell factor receptor, GIST, gastrointestinal stromal tumors, P10721, TRANSFERASE ;; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	32.78 Å
回转半径 Rg (电子) rg_electron	32.33 Å
零角强度 I(0) i0	68971500.00
分子量 molecular_weight	66793.0 kDa
排除体积 excluded_volume	83912 Å³
包络体积 envelope_volume	113030 Å³
水化壳体积 shell_volume	29984 Å³
包络直径 envelope_diameter	113.5 Å
壳层 Rg shell_rg	37.87 Å
包络 Rg envelope_rg	32.17 Å
形状 Rg shape_rg	32.31 Å
总 Rg total_rg	32.90 Å
总原子数 total_atoms	4707
残基数 n_residues	592
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/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	113.0 Å
Rg (实空间) rg_real	33.07 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	6.8970e+07
I(0) 误差 (实空间) i0_real_error	1.0460e+06
Rg (倒空间) rg_reciprocal	32.95 Å
I(0) (倒空间) i0_reciprocal	68960000.0000
解质量估计 total_estimate	0.6095
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	28.2 Å
偏度 Skewness skewness	0.452
峰度 Kurtosis kurtosis	-0.488
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17260000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.680; Smooth: 0.825

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Mast/stem cell growth factor receptor Kit
分子量 formula_weight	37194.4 kDa
EC 编号 ec_number	2.7.10.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5176

GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;(1~{S})-~{N}-ethyl-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethanamine ;
分子量 formula_weight	526.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	371

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7. 引用文献 (1)

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晶胞边长 a length_a	59.220 Å
晶胞边长 b length_b	59.220 Å
晶胞边长 c length_c	192.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.770 Å
最低分辨率 resolution_low	43.530 Å
R 因子 r_factor	0.1826
R_work r_work	0.1814
R_free r_free	0.2063

fit	/app/data/saxs_computation/pq/8pqc/8pqc.fit
pddf	/app/data/pr_computation/pq/8pqc/8pqc.pr.out
profile	/app/data/saxs_computation/pq/8pqc/8pqc.dat

c-KIT kinase domain in complex with avapritinib derivative 9

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction