Binding Site Information of Target
Target General Information | Top | ||||
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Target ID | T05114 | Target Info | |||
Target Name | Chymase (CYM) | ||||
Synonyms | Mast cell protease I; CYH; Alpha-chymase | ||||
Target Type | Clinical trial Target | ||||
Gene Name | CMA1 | ||||
Biochemical Class | Peptidase | ||||
UniProt ID |
Drug Binding Sites of Target | Top | |||||
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Ligand Name: (3s)-3-{3-[(6-Bromo-2-Oxo-2,3-Dihydro-1h-Indol-4-Yl)methyl]-2-Oxo-2,3-Dihydro-1h-Benzimidazol-1-Yl}hexanoic Acid | Ligand Info | |||||
Structure Description | Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-bromo-2-oxo-2,3-dihydro-1H-indol-4-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}hexanoic acid | PDB:4K69 | ||||
Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [1] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLGR 134 MCRVAGWGRT144 GVLKPGSDTL155 QEVKLRLMDP165 QACSHFRDFD177 HNLQLCVGNP 185A RKTKSAFKGD194 SGGPLLCAGA208 AQGIVSYGRS218 DAKPPAVFTR230 ISHYQPWINQ 240 ILQAN
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ILE35
4.188
LYS40
4.086
PHE41
4.183
CYS42
3.565
HIS57
3.231
CYS58
4.296
LEU99
3.992
SER189
4.343
ALA190
3.189
PHE191
3.690
LYS192
2.683
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Ligand Name: 6-Bromooxindole | Ligand Info | |||||
Structure Description | Crystal Structure of Human Chymase in Complex with Fragment 6-bromo-1,3-dihydro-2H-indol-2-one | PDB:4K60 | ||||
Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [1] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTNGPSKFCG43 GFLIRRNFVL53 TAAHCAGRSI64 TVTLGAHNIT 74 EEEDTWQKLE84 VIKQFRHPKY94 NTSTLHHDIM104 LLKLKEKASL114 TLAVGTLPFV 130 PPGRMCRVAG140 WGRTGVLKPG151 SDTLQEVKLR161 LMDPQACSHF173 RDFDHNLQLC 182 VGNPRKTKSA190 FKGDSGGPLL200 CAGAAQGIVS214 YGRSDAKPPA226 VFTRISHYQP 236 WINQILQAN
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Ligand Name: (2S)-2-Hydroxybutanedioic acid | Ligand Info | |||||
Structure Description | Human Chymase - Fynomer Complex | PDB:4AG2 | ||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
PDB Sequence |
IIGGTECKPH
10 SRPYMAYLEI20 VTSNGPSKFC30 GGFLIRRNFV40 LTAAHCAGRS50 ITVTLGAHNI 60 TEEEDTWQKL70 EVIKQFRHPK80 YNTSTLHHDI90 MLLKLKEKAS100 LTLAVGTLPF 110 PNFVPPGRMC123 RVAGWGRTGV133 LKPGSDTLQE143 VKLRLMDPQA153 CSHFRDFDHN 163 LQLCVGNPRK173 TKSAFKGDSG183 GPLLCAGVAQ193 GIVSYGRSDA203 KPPAVFTRIS 213 HYRPWINQIL223 QAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LMR or .LMR2 or .LMR3 or :3LMR;style chemicals stick;color identity;select .A:156 or .A:157 or .A:158 or .A:159 or .A:200; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: (S)-[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-{[(E)-2-(3,4-difluorophenyl)ethenyl]amino}-2-oxoethyl]methylphosphinic acid | Ligand Info | |||||
Structure Description | X-ray structure of human chymase in complex with small molecule inhibitor. | PDB:3N7O | ||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [3] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 PSFVPPGRMC136 RVAGWGRTGV146 LKPGSDTLQE157 VKLRLMDPQA167 CSHFRDFDHN 178 LQLCVGNPRK186 TKSAFKGDSG196 GPLLCAGAAQ210 GIVSYGRSDA220 KPPAVFTRIS 232 HYQPWINQIL242 QAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N7O or .N7O2 or .N7O3 or :3N7O;style chemicals stick;color identity;select .A:40 or .A:42 or .A:57 or .A:94 or .A:95 or .A:96 or .A:99 or .A:100 or .A:102 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS40
2.752
CYS42
4.863
HIS57
2.661
TYR94
3.125
ASN95
3.078
THR96
3.176
LEU99
3.542
HIS100
4.755
ASP102
3.322
ALA190
3.563
PHE191
3.613
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Ligand Name: 4-[(1R)-1-[[(6R)-6-[(5-chloro-2-methoxyphenyl)methyl]-3-(ethoxyamino)-7-oxo-5,6-dihydro-2H-1,4-diazepine-1-carbonyl]amino]propyl]benzoic acid | Ligand Info | |||||
Structure Description | Human chymase in complex with 3-(ethoxyimino)-7-oxo-1,4-diazepane derivative | PDB:5YJP | ||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [4] |
PDB Sequence |
IIGGTESKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 VPPGRMCRVA139 GWGRTGVLKP150 GSDTLQEVKL160 RLMDPQACSH172 FRDFDHNLQL 181 CVGNPRKTKS189 AFKGDSGGPL199 LCAGVAQGIV213 SYGRSDAKPP225 AVFTRISHYR 235 PWINQILQAN245
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8W6 or .8W62 or .8W63 or :38W6;style chemicals stick;color identity;select .A:35 or .A:40 or .A:41 or .A:42 or .A:57 or .A:58 or .A:94 or .A:99 or .A:102 or .A:143 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE35
4.620
LYS40
4.176
PHE41
3.543
CYS42
3.681
HIS57
3.473
CYS58
4.124
TYR94
3.741
LEU99
3.912
ASP102
3.534
ARG143
2.733
SER189
4.322
ALA190
3.569
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Ligand Name: 6-Chloroisoindolin-1-one | Ligand Info | |||||
Structure Description | Crystal Structure of Human Chymase in Complex with Fragment Inhibitor 6-chloro-2,3-dihydro-1H-isoindol-1-one | PDB:4K5Z | ||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 VPPGRMCRVA139 GWGRTGVLKP150 GSDTLQEVKL160 RLMDPQACSH172 FRDFDHNLQL 181 CVGNPRKTKS189 AFKGDSGGPL199 LCAGAAQGIV213 SYGRSDAKPP225 AVFTRISHYQ 235 PWINQILQAN245
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1P7 or .1P72 or .1P73 or :31P7;style chemicals stick;color identity;select .A:57 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:220 or .A:226 or .A:228; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 2-[3-({Methyl[1-(2-naphthoyl)piperidin-4-YL]amino}carbonyl)-2-naphthyl]-1-(1-naphthyl)-2-oxoethylphosphonic acid | Ligand Info | |||||
Structure Description | A Dual Inhibitor of the Leukocyte Proteases Cathepsin G and Chymase with Therapeutic Efficacy in Animals Models of Inflammation | PDB:1T31 | ||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [5] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 PSQKNFVPPG133 RMCRVAGWGR143 TGVLKPGSDT154 LQEVKLRLMD164 PQACSHFRDF 176 DHNLQLCVGN185 PRKTKSAFKG193 DSGGPLLCAG207 AAQGIVSYGR217 SDAKPPAVFT 229 RISHYQPWIN239 QILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OHH or .OHH2 or .OHH3 or :3OHH;style chemicals stick;color identity;select .A:40 or .A:41 or .A:42 or .A:57 or .A:58 or .A:94 or .A:96 or .A:99 or .A:102 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS40
2.567
PHE41
4.598
CYS42
3.981
HIS57
2.962
CYS58
4.631
TYR94
3.993
THR96
3.823
LEU99
3.848
ASP102
4.467
SER189
4.766
ALA190
3.234
PHE191
3.595
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Ligand Name: example 32 [WO2011078413] | Ligand Info | |||||
Structure Description | Human chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepane derivative | PDB:5YJM | ||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [4] |
PDB Sequence |
IIGGTESKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 PGRMCRVAGW141 GRTGVLKPGS152 DTLQEVKLRL162 MDPQACSHFR174 DFDHNLQLCV 183 GNPRKTKSAF191 KGDSGGPLLC201 AGVAQGIVSY215 GRSDAKPPAV227 FTRISHYRPW 237 INQILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8W3 or .8W32 or .8W33 or :38W3;style chemicals stick;color identity;select .A:35 or .A:40 or .A:41 or .A:42 or .A:57 or .A:58 or .A:94 or .A:95 or .A:96 or .A:99 or .A:102 or .A:143 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226 or .A:228; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE35
4.007
LYS40
4.042
PHE41
2.952
CYS42
3.388
HIS57
3.392
CYS58
4.296
TYR94
3.465
ASN95
4.055
THR96
4.337
LEU99
3.414
ASP102
3.361
ARG143
2.926
SER189
4.304
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Ligand Name: Phenylmethanesulfonic acid | Ligand Info | |||||
Structure Description | CRYSTAL STRUCTURE OF PMSF-TREATED HUMAN CHYMASE AT 1.9 ANGSTROMS RESOLUTION | PDB:1KLT | ||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | Yes | [6] |
PDB Sequence |
IIGGTESKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 PSQFNFVPPG133 RMCRVAGWGR143 TGVLKPGSDT154 LQEVKLRLMD164 PQACSHFRDF 176 DHNLQLCVGN185 PRKTKSAFKG193 DSGGPLLCAG207 VAQGIVSYGR217 SDAKPPAVFT 229 RISHYRPWIN239 QILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PMS or .PMS2 or .PMS3 or :3PMS;style chemicals stick;color identity;select .A:42 or .A:57 or .A:58 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:226; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 4-{3-[(4-Methyl-1-Benzothiophen-3-Yl)methyl]-2-Oxo-2,3-Dihydro-1h-Benzimidazol-1-Yl}butanoic Acid | Ligand Info | |||||
Structure Description | Crystal Structure of Human Chymase with Benzimidazolone Inhibitor | PDB:3S0N | ||||
Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | Yes | [7] |
PDB Sequence |
IIGGTECKPH
10 SRPYMAYLEI20 VTSNGPSKFC30 GGFLIRRNFV40 LTAAHCAGRS50 ITVTLGAHNI 60 TEEEDTWQKL70 EVIKQFRHPK80 YNTSTLHHDI90 MLLKLKEKAS100 LTLAVGTLPF 110 PSQKNFVPPG120 RMCRVAGWGR130 TGVLKPGSDT140 LQEVKLRLMD150 PQACSHFRDF 160 DHNLQLCVGN170 PRKTKSAFKG180 DSGGPLLCAG190 AAQGIVSYGR200 SDAKPPAVFT 210 RISHYQPWIN220 QILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0BB or .0BB2 or .0BB3 or :30BB;style chemicals stick;color identity;select .A:28 or .A:45 or .A:81 or .A:86 or .A:89 or .A:176 or .A:177 or .A:178 or .A:179 or .A:180 or .A:181 or .A:182 or .A:196 or .A:197 or .A:198 or .A:199 or .A:200 or .A:201 or .A:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 6-Chlorooxindole | Ligand Info | |||||
Structure Description | Crystal Structure of Human Chymase in Complex with Fragment Inhibitor 6-chloro-1,3-dihydro-2H-indol-2-one | PDB:4K2Y | ||||
Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPP 132 GRMCRVAGWG142 RTGVLKPGSD153 TLQEVKLRLM163 DPQACSHFRD175 FDHNLQLCVG 184 NPRKTKSAFK192 GDSGGPLLCA202 GAAQGIVSYG216 RSDAKPPAVF228 TRISHYQPWI 238 NQILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ES2 or .ES22 or .ES23 or :3ES2;style chemicals stick;color identity;select .A:189 or .A:190 or .A:191 or .A:192 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: [(1s)-1-(5-Chloro-1-Benzothien-3-Yl)-2-(2-Naphthylamino)-2-Oxoethyl]phosphonic Acid | Ligand Info | |||||
Structure Description | Discovery of Potent, Orally Active, Nonpeptide Inhibitors of Human Mast Cell Chymase by Using Structure-Based Drug Design | PDB:2HVX | ||||
Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | Yes | [8] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 PSQKNFVPPG133 RMCRVAGWGR143 TGVLKPGSDT154 LQEVKLRLMD164 PQACSHFRDF 176 DHNLQLCVGN185 PRKTKSAFKG193 DSGGPLLCAG207 AAQGIVSYGR217 SDAKPPAVFT 229 RISHYQPWIN239 QILQAN
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DRX or .DRX2 or .DRX3 or :3DRX;style chemicals stick;color identity;select .A:57 or .A:94 or .A:95 or .A:96 or .A:99 or .A:100 or .A:102 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226 or .A:228; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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HIS57
2.757
TYR94
3.295
ASN95
3.435
THR96
3.473
LEU99
2.982
HIS100
4.923
ASP102
3.399
SER189
4.671
ALA190
2.766
PHE191
3.435
LYS192
2.647
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Ligand Name: 4-({1-[(4-Methyl-1-Benzothiophen-3-Yl)methyl]-1h-Benzimidazol-2-Yl}sulfanyl)butanoic Acid | Ligand Info | |||||
Structure Description | Crystal Structure of the human Chymase with TJK002 | PDB:4KP0 | ||||
Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [9] |
PDB Sequence |
IIGGTECKPH
25 SRPYMAYLEI35 VTSNGPSKFC42 GGFLIRRNFV52 LTAAHCAGRS63 ITVTLGAHNI 73 TEEEDTWQKL83 EVIKQFRHPK93 YNTSTLHHDI103 MLLKLKEKAS113 LTLAVGTLPF 123 VPPGRMCRVA139 GWGRTGVLKP150 GSDTLQEVKL160 RLMDPQACSH172 FRDFDHNLQL 181 CVGNPRKTKS189 AFKGDSGGPL199 LCAGVAQGIV213 SYGRSDAKPP225 AVFTRISHYR 235 PWINQILQAN245
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KPK or .KPK2 or .KPK3 or :3KPK;style chemicals stick;color identity;select .A:40 or .A:41 or .A:42 or .A:57 or .A:58 or .A:99 or .A:102 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:226; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS40
4.384
PHE41
3.792
CYS42
4.054
HIS57
2.616
CYS58
4.465
LEU99
3.821
ASP102
4.836
SER189
4.872
ALA190
3.431
PHE191
3.362
LYS192
3.148
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References | Top | ||||
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REF 1 | Discovery of potent, selective chymase inhibitors via fragment linking strategies. J Med Chem. 2013 Jun 13;56(11):4465-81. | ||||
REF 2 | Generation, characterization and structural data of chymase binding proteins based on the human Fyn kinase SH3 domain. MAbs. 2012 Jul-Aug;4(4):497-508. | ||||
REF 3 | Potency variation of small-molecule chymase inhibitors across species. Biochem Pharmacol. 2010 Oct 1;80(7):1033-41. | ||||
REF 4 | Structure-based design, synthesis, and binding mode analysis of novel and potent chymase inhibitors. Bioorg Med Chem Lett. 2018 Jan 15;28(2):188-192. | ||||
REF 5 | A novel, potent dual inhibitor of the leukocyte proteases cathepsin G and chymase: molecular mechanisms and anti-inflammatory activity in vivo. J Biol Chem. 2005 May 6;280(18):18001-7. | ||||
REF 6 | Crystal structure of phenylmethanesulfonyl fluoride-treated human chymase at 1.9 A. Biochemistry. 1997 Nov 25;36(47):14318-24. | ||||
REF 7 | Benzimidazolone as potent chymase inhibitor: modulation of reactive metabolite formation in the hydrophobic (P1) region. Bioorg Med Chem Lett. 2011 Aug 1;21(15):4533-9. | ||||
REF 8 | Discovery of potent, selective, orally active, nonpeptide inhibitors of human mast cell chymase. J Med Chem. 2007 Apr 19;50(8):1727-30. | ||||
REF 9 | Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor. J Synchrotron Radiat. 2013 Nov;20(Pt 6):914-8. |
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