9h79

;Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. ;

Method: X-RAY DIFFRACTION D_max: 123.0 Å Quality: GOOD

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	9h79
沉积日期 deposition_date	2024-10-27
最后修订 last_revision	2025-11-05
结构标题 title	;Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. ;
关键词 keywords	Thrombin, protease, combinatorial design of nanoscale libraries, small molecules inhibitors, HYDROLASE; HYDROLASE
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	37.57 Å
回转半径 Rg (电子) rg_electron	37.18 Å
零角强度 I(0) i0	528302000.00
分子量 molecular_weight	124510.0 kDa
排除体积 excluded_volume	120180 Å³
包络体积 envelope_volume	214630 Å³
水化壳体积 shell_volume	47938 Å³
包络直径 envelope_diameter	131.7 Å
壳层 Rg shell_rg	43.46 Å
包络 Rg envelope_rg	36.64 Å
形状 Rg shape_rg	37.18 Å
总 Rg total_rg	37.46 Å
总原子数 total_atoms	9396
残基数 n_residues	1139
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	123.0 Å
Rg (实空间) rg_real	37.53 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	5.2830e+08
I(0) 误差 (实空间) i0_real_error	8.8310e+06
Rg (倒空间) rg_reciprocal	37.56 Å
I(0) (倒空间) i0_reciprocal	528300000.0000
解质量估计 total_estimate	0.8799
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	55.6 Å
偏度 Skewness skewness	0.222
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	589300000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.858

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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 (6)

Entity 1 polymer

描述 description	Thrombin light chain
分子量 formula_weight	5641.2 kDa
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,C,E,G
原子数 atom_count	9428

TATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

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	Homo sapiens

Entity 2 polymer

描述 description	Prothrombin
分子量 formula_weight	29780.2 kDa
EC 编号 ec_number	3.4.21.5
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	B,D,F,H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

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	Homo sapiens

Entity 3 non-polymer

描述 description	;~{N}-[(3~{S})-4-[3-(2-azanyl-2-oxidanylidene-ethyl)sulfanylpropylamino]-3-[2-(3-chlorophenyl)ethanoylamino]-4-oxidanylidene-butyl]-5-chloranyl-thiophene-2-carboxamide ;
分子量 formula_weight	545.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 6 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	32

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7. 引用文献 (1)

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晶胞边长 a length_a	75.700 Å
晶胞边长 b length_b	85.325 Å
晶胞边长 c length_c	214.280 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	16

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

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	44.370 Å
R 因子 r_factor	0.2074
R_work r_work	0.2043
R_free r_free	0.2662

fit	/app/data/saxs_computation/h7/9h79/9h79.fit
pddf	/app/data/pr_computation/h7/9h79/9h79.pr.out
profile	/app/data/saxs_computation/h7/9h79/9h79.dat

;Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP2, discovered by a novel rapid nanoscale library screening. ;

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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)