8fh4

;Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile ;

Method: X-RAY DIFFRACTION D_max: 134.3 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	8fh4
沉积日期 deposition_date	2022-12-13
结构标题 title	;Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile ;
关键词 keywords	inhibitor, hematopoietic, kinase, 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	42.84 Å
回转半径 Rg (电子) rg_electron	42.51 Å
零角强度 I(0) i0	241468000.00
分子量 molecular_weight	131240.0 kDa
排除体积 excluded_volume	166540 Å³
包络体积 envelope_volume	242110 Å³
水化壳体积 shell_volume	50489 Å³
包络直径 envelope_diameter	137.0 Å
壳层 Rg shell_rg	44.21 Å
包络 Rg envelope_rg	41.42 Å
形状 Rg shape_rg	42.52 Å
总 Rg total_rg	42.58 Å
总原子数 total_atoms	9239
残基数 n_residues	1157
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	134.3 Å
Rg (实空间) rg_real	44.01 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	2.3940e+08
I(0) 误差 (实空间) i0_real_error	3.5810e+06
Rg (倒空间) rg_reciprocal	42.84 Å
I(0) (倒空间) i0_reciprocal	241500000.0000
解质量估计 total_estimate	0.6804
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	54.4 Å
偏度 Skewness skewness	0.232
峰度 Kurtosis kurtosis	-0.666
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	2.2330
最高正则化参数 α highest_alpha	19650000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 0.902; Sysdev: 0.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.307

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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 (4)

Entity 1 polymer

描述 description	Mitogen-activated protein kinase kinase kinase kinase 1
分子量 formula_weight	37141.7 kDa
EC 编号 ec_number	2.7.11.1
突变 mutation	T165E, S171E
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10077

MASHHHHHHDYDGATTENLYFQGSMDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNPGKGPSIGDIEDEE

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	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	(3P)-3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undecan-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile
分子量 formula_weight	422.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	834

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7. 引用文献 (1)

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晶胞边长 a length_a	57.756 Å
晶胞边长 b length_b	70.505 Å
晶胞边长 c length_c	86.042 Å
晶胞夹角 α angle_alpha	97.66 °
晶胞夹角 β angle_beta	108.73 °
晶胞夹角 γ angle_gamma	92.66 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.827 Å
最低分辨率 resolution_low	69.560 Å
R 因子 r_factor	0.1888
R_work r_work	0.1874
R_free r_free	0.2152

fit	/app/data/saxs_computation/fh/8fh4/8fh4.fit
pddf	/app/data/pr_computation/fh/8fh4/8fh4.pr.out
profile	/app/data/saxs_computation/fh/8fh4/8fh4.dat

;Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with 3-[6-chloro-4-(9-methyl-1-oxa-4,9-diazaspiro[5.5]undec-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile ;

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