3be9

Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities

Method: X-RAY DIFFRACTION D_max: 67.4 Å Quality: GOOD

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Casein kinase II subunit alpha

Zea mays

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白单体单体蛋白 × 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 1–332	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P04 19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.05M Sodium Acetate, 0.10M TRISHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 2.00 Å R-free 0.228

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3BE9	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1DAW CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPHA-SUBUNIT) AND MG-AMPPNP 提交 1999-11-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：CATALYTIC SUBUNIT	未记录	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 3350, SODIUM ACETATE, TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.20 Å R-free 0.285
1DAY CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPHA-SUBUNIT) AND MG-GMPPNP 提交 1999-11-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：CATALYTIC SUBUNIT	未记录	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 3350, SODIUM ACETATE, TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.20 Å R-free 0.290
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. 提交 2000-01-07	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–332（332 aa）链 B 1–332（332 aa）	未记录	AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	分辨率 3.16 Å R-free 0.289
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. 提交 2000-01-07	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 C 1–332（332 aa）链 D 1–332（332 aa）	未记录	AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	分辨率 3.16 Å R-free 0.289
1F0Q CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN 提交 2000-05-17	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	EMO 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	分辨率 2.63 Å R-free 0.273
1J91 Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the ATP-competitive inhibitor 4,5,6,7-tetrabromobenzotriazole 提交 2001-05-23	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	TBS 4,5,6,7-TETRABROMOBENZOTRIAZOLE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.22 Å R-free 0.268
1J91 Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the ATP-competitive inhibitor 4,5,6,7-tetrabromobenzotriazole 提交 2001-05-23	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–332（332 aa）	未记录	TBS 4,5,6,7-TETRABROMOBENZOTRIAZOLE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.22 Å R-free 0.268
1JAM Crystal structure of apo-form of Z. Mays CK2 protein kinase alpha subunit 提交 2001-05-31	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；287 K；30% PEG 4000, 200 mM sodium acetate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K	分辨率 2.18 Å R-free 0.248
1LP4 Crystal structure of a binary complex of the catalytic subunit of protein kinase CK2 with Mg-AMPPNP 提交 2002-05-07	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；PEG3350, SODIUM ACETATE, TRIS/HCL, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.86 Å R-free 0.244
1LPU Low Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays 提交 2002-05-08	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；PEG3350, Tris/HCl, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.86 Å R-free 0.248
1LR4 Room Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays 提交 2002-05-14	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.00 Å R-free 0.237
1M2P Crystal structure of 1,8-di-hydroxy-4-nitro-anthraquinone/CK2 kinase complex 提交 2002-06-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–326（325 aa）片段：Catlytic subunit	未记录	HNA 1,8-DI-HYDROXY-4-NITRO-ANTHRAQUINONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.00 Å R-free 0.243
1M2Q Crystal structure of 1,8-di-hydroxy-4-nitro-xanten-9-one/CK2 kinase complex 提交 2002-06-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：Catlytic subunit	未记录	MNX 1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.79 Å R-free 0.232
1M2R Crystal structure of 5,8-di-amino-1,4-di-hydroxy-anthraquinone/CK2 kinase complex 提交 2002-06-25	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：catalytic subunit	未记录	MNY 5,8-DI-AMINO-1,4-DIHYDROXY-ANTHRAQUINONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.70 Å R-free 0.216
1OM1 Crystal structure of maize CK2 alpha in complex with IQA 提交 2003-02-24	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	IQA (5-OXO-5,6-DIHYDRO-INDOLO[1,2-A]QUINAZOLIN-7-YL)-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, SODIUM ACETATE, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.68 Å R-free 0.227
1ZOE Crystal structure of protein kinase CK2 in complex with TBB-derivatives inhibitors 提交 2005-05-13	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–332（332 aa）	未记录	CL CHLORIDE ION × 2 K25 4,5,6,7-TETRABROMO-N,N-DIMETHYL-1H-BENZIMIDAZOL-2-AMINE × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.77 Å R-free 0.277
1ZOG Crystal structure of protein kinase CK2 in complex with TBB-derivatives 提交 2005-05-13	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–332（332 aa）	未记录	K37 4,5,6,7-TETRABROMO-2-(METHYLSULFANYL)-1H-BENZIMIDAZOLE × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.30 Å R-free 0.294
1ZOH Crystal structure of protein kinase CK2 in complex with TBB-derivatives inhibitors 提交 2005-05-13	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–332（332 aa）	未记录	NA SODIUM ION × 2 CL CHLORIDE ION × 4 K44 5,6,7,8-TETRABROMO-1-METHYL-2,3-DIHYDRO-1H-IMIDAZO[1,2-A]BENZIMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.81 Å R-free 0.221
2OXD Protein kinase CK2 in complex with tetrabromobenzoimidazole K17, K22 and K32 inhibitors 提交 2007-02-20	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	K32 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	分辨率 2.30 Å R-free 0.273
2OXX Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 提交 2007-02-21	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	K22 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-THIONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.30 Å R-free 0.270
2OXY Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 提交 2007-02-21	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	K17 4,5,6,7-TETRABROMO-BENZIMIDAZOLE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.81 Å R-free 0.269
2OXY Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 提交 2007-02-21	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–332（332 aa）	未记录	K17 4,5,6,7-TETRABROMO-BENZIMIDAZOLE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.81 Å R-free 0.269
2PVH Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P19 N,N'-DIPHENYLPYRAZOLO[1,5-A][1,3,5]TRIAZINE-2,4-DIAMINE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；18% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 2.20 Å R-free 0.236
2PVJ Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P44 2-(CYCLOHEXYLMETHYLAMINO)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；12% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 1.70 Å R-free 0.218
2PVK Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P45 2-(4-CHLOROBENZYLAMINO)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 1.90 Å R-free 0.244
2PVL Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P55 2-(4-ETHYLPIPERAZIN-1-YL)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 1.90 Å R-free 0.289
2PVM Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P29 4-(2-(1H-IMIDAZOL-4-YL)ETHYLAMINO)-2-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；12% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 2.00 Å R-free 0.225
2PVN Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 提交 2007-05-09	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	突变：V256A 非标准单体：是（mmCIF未提供具体位点）	P63 N-(3-(8-CYANO-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZIN-2-YLAMINO)PHENYL)ACETAMIDE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；16% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	分辨率 2.00 Å R-free 0.308
2QC6 Protein kinase CK2 in complex with DBC 提交 2007-06-19	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	非标准单体：是（mmCIF未提供具体位点）	G12 3,8-DIBROMO-7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 8；293 K；10-20% PEG4000, 0.2 M Sodium Acetate, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 293.0K	分辨率 1.85 Å R-free 0.268
3FL5 Protein kinase CK2 in complex with the inhibitor Quinalizarin 提交 2008-12-18	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	非标准单体：是（mmCIF未提供具体位点）	PEG DI(HYDROXYETHYL)ETHER × 1 TXQ 1,2,5,8-tetrahydroxyanthracene-9,10-dione × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 4000, 200mM Na-acetate, 100mM Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.30 Å R-free 0.235
3KXG Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor 3,4,5,6,7-pentabromo-1H-indazole (K64) 提交 2009-12-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：ALPHA SUBUNIT	非标准单体：是（mmCIF未提供具体位点）	K6X 3,4,5,6,7-pentabromo-1H-indazole × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.70 Å R-free 0.263
3KXH Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor (2-dymethylammino-4,5,6,7-tetrabromobenzoimidazol-1yl-acetic acid (K66) 提交 2009-12-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：ALPHA SUBUNIT	非标准单体：是（mmCIF未提供具体位点）	K66 [4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzimidazol-1-yl]acetic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.70 Å R-free 0.266
3KXM Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor K74 提交 2009-12-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：ALPHA SUBUNIT	未记录	K74 N-methyl-2-[(4,5,6,7-tetrabromo-1-methyl-1H-benzimidazol-2-yl)sulfanyl]acetamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.75 Å R-free 0.282
3KXN Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor tetraiodobenzimidazole (K88) 提交 2009-12-03	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–328（327 aa）片段：ALPHA SUBUNIT	未记录	K8X 4,5,6,7-tetraiodo-1H-benzimidazole × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.00 Å R-free 0.264
3PVG Crystal structure of Z. mays CK2 alpha subunit in complex with the inhibitor 4,5,6,7-tetrabromo-1-carboxymethylbenzimidazole (K68) 提交 2010-12-07	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）片段：alpha subunit	非标准单体：是（mmCIF未提供具体位点）	K68 (4,5,6,7-tetrabromo-1H-benzimidazol-1-yl)acetic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.50 Å R-free 0.211
3PWD Crystal structure of maize CK2 in complex with NBC (Z1) 提交 2010-12-08	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	CZ0 8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K	分辨率 2.20 Å R-free 0.230
3PZH Crystal structure of maize CK2 alpha in complex with emodin at 1.92 A resolution 提交 2010-12-14	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	非标准单体：是（mmCIF未提供具体位点）	EMO 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K	分辨率 1.92 Å R-free 0.209
4ANM Complex of CK2 with a CDC7 inhibitor 提交 2012-03-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–332（331 aa）片段：KINASE DOMAIN, RESIDUES 2-332	未记录	WUL 8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 8；20% PEG4K, 200 MM NAOAC, 100 MM TRIS, PH 8.0	分辨率 1.70 Å R-free 0.202
4DGM Crystal Structure of maize CK2 in complex with the inhibitor apigenin 提交 2012-01-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–327（326 aa）	未记录	EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 AGI 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate, pH 8, VAPOR DIFFUSION, temperature 293K	分辨率 1.65 Å R-free 0.252
4DGN Crystal Structure of maize CK2 in complex with the inhibitor luteolin 提交 2012-01-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–327（326 aa）	非标准单体：是（mmCIF未提供具体位点）	LU2 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate, pH 8, VAPOR DIFFUSION, temperature 293K	分辨率 1.75 Å R-free 0.214
4RLK Crystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate 提交 2014-10-17	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–332（332 aa）	未记录	GOL GLYCEROL × 3 ACT ACETATE ION × 2 E91 4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Reservoir: 20 % PEG 4000, 0.2 M sodium acetate, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.24 Å R-free 0.175
6QS5 Crystal Structure of maize CK2 in complex with tyrphostin AG99 提交 2019-02-20	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–326（325 aa）	未记录	JGB (~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate	分辨率 1.96 Å R-free 0.219

共 39 个其他 PDB 条目、42 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	CSK2A_MAIZE
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 21–352； UniProt 1–332

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3be9
沉积日期 deposition_date	2007-11-16
结构标题 title	Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities
关键词 keywords	;STRUCTURE-BASED DRUG DESIGN, ENZYME-INHIBITOR COMPLEX, CASEIN KINASE II, PROTEIN KINASE CK2, ATP-binding, Nucleotide-binding, Serine/threonine-protein kinase, Transferase ;; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	21.61 Å
回转半径 Rg (电子) rg_electron	20.33 Å
零角强度 I(0) i0	24920100.00
分子量 molecular_weight	39082.0 kDa
排除体积 excluded_volume	49316 Å³
包络体积 envelope_volume	56504 Å³
水化壳体积 shell_volume	22958 Å³
包络直径 envelope_diameter	69.1 Å
壳层 Rg shell_rg	27.20 Å
包络 Rg envelope_rg	20.62 Å
形状 Rg shape_rg	20.32 Å
总 Rg total_rg	21.27 Å
总原子数 total_atoms	2761
残基数 n_residues	327
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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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	67.4 Å
Rg (实空间) rg_real	21.51 Å
Rg 误差 (实空间) rg_real_error	0.39 Å
I(0) (实空间) i0_real	2.4920e+07
I(0) 误差 (实空间) i0_real_error	2.9950e+05
Rg (倒空间) rg_reciprocal	21.53 Å
I(0) (倒空间) i0_reciprocal	24920000.0000
解质量估计 total_estimate	0.8238
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	25.8 Å
偏度 Skewness skewness	0.237
峰度 Kurtosis kurtosis	-0.373
角度范围 angular_range	— – 0.3700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6332000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	Casein kinase II subunit alpha
分子量 formula_weight	41450.5 kDa
EC 编号 ec_number	2.7.11.1
突变 mutation	V256A
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3007

MGSSHHHHHHSSGLVPRGSHMSKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLCGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNAYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENSRTRA

来源 Source

来源生物 organism	Zea mays
通用名 common_name	Maize
NCBI 分类编号 ncbi_taxonomy_id	4577
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	;19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one ;
分子量 formula_weight	363.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 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	246

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7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	3be9A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

结构域编号 domain_id	3be9A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

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8. 引用文献 (1)

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晶胞边长 a length_a	143.327 Å
晶胞边长 b length_b	59.578 Å
晶胞边长 c length_c	44.835 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.42 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	32.700 Å
R 因子 r_factor	—
R_work r_work	0.1900
R_free r_free	0.2280

fit	/app/data/saxs_computation/be/3be9/3be9.fit
pddf	/app/data/pr_computation/be/3be9/3be9.pr.out
profile	/app/data/saxs_computation/be/3be9/3be9.dat