8g3e

;Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) ;

Method: X-RAY DIFFRACTION D_max: 110.3 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	8g3e
沉积日期 deposition_date	2023-02-07
结构标题 title	;Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) ;
关键词 keywords	WDR5, MYC, WBM, small molecule, ONCOPROTEIN-INHIBITOR complex; ONCOPROTEIN/INHIBITOR
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	28.97 Å
回转半径 Rg (电子) rg_electron	28.50 Å
零角强度 I(0) i0	73350400.00
分子量 molecular_weight	68500.0 kDa
排除体积 excluded_volume	86184 Å³
包络体积 envelope_volume	105400 Å³
水化壳体积 shell_volume	30893 Å³
包络直径 envelope_diameter	116.0 Å
壳层 Rg shell_rg	35.39 Å
包络 Rg envelope_rg	29.06 Å
形状 Rg shape_rg	28.49 Å
总 Rg total_rg	29.21 Å
总原子数 total_atoms	4829
残基数 n_residues	617
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	110.3 Å
Rg (实空间) rg_real	29.06 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	7.3350e+07
I(0) 误差 (实空间) i0_real_error	1.2440e+06
Rg (倒空间) rg_reciprocal	29.02 Å
I(0) (倒空间) i0_reciprocal	73350000.0000
解质量估计 total_estimate	0.6992
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.1 Å
偏度 Skewness skewness	0.405
峰度 Kurtosis kurtosis	-0.487
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24130000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.524; Smooth: 0.000

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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	WD repeat-containing protein 5
分子量 formula_weight	34663.2 kDa
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	5480

SNASATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

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

Entity 2 non-polymer

描述 description	(1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide
分子量 formula_weight	432.4 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	620

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7. 引用文献 (1)

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晶胞边长 a length_a	46.662 Å
晶胞边长 b length_b	62.276 Å
晶胞边长 c length_c	64.381 Å
晶胞夹角 α angle_alpha	114.09 °
晶胞夹角 β angle_beta	91.08 °
晶胞夹角 γ angle_gamma	110.17 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.330 Å
最低分辨率 resolution_low	32.350 Å
R 因子 r_factor	0.1407
R_work r_work	0.1391
R_free r_free	0.1705

fit	/app/data/saxs_computation/g3/8g3e/8g3e.fit
pddf	/app/data/pr_computation/g3/8g3e/8g3e.pr.out
profile	/app/data/saxs_computation/g3/8g3e/8g3e.dat

;Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) ;

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