[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCrystallographic Fragment Screening of an Entire Library
Journal, issue, pagesTo Be Published
Publish dateFeb 10, 2015 (structure data deposition date)
AuthorsHeine, A. / Knoerlein, A. / Schiebel, J. / Klebe, G.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution0.99 - 1.754 Å
Structure data

PDB-4y35:
Endothiapepsin in complex with fragment 290
Method: X-RAY DIFFRACTION / Resolution: 1.457 Å

PDB-4y36:
Endothiapepsin in complex with fragment 4
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-4y37:
Endothiapepsin in complex with fragement 305
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-4y39:
Endothiapepsin in complex with fragment 75
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-4y3e:
Endothiapepsin in complex with fragment 5
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-4y3f:
Endothiapepsin in complex with fragment 78
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-4y3g:
Endothiapepsin in complex with fragment 285
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-4y3m:
Endothiapepsin in complex with fragment 103
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-4y3n:
Endothiapepsin in complex with fragment 273
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-4y3p:
Endothiapepsin in complex with fragment 17
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-4y3q:
Endothiapepsin in complex with fragment 109
Method: X-RAY DIFFRACTION / Resolution: 1.17 Å

PDB-4y3r:
Endothiapepsin in complex with fragment 306
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-4y3s:
Endothiapepsin in complex with fragment 266
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-4y3w:
Endothiapepsin in complex with fragment 35
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-4y3x:
Endothiapepsin in complex with fragment 171
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-4y3z:
Endothiapepsin in complex with fragment 41
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-4y41:
Endothiapepsin in complex with fragment 112
Method: X-RAY DIFFRACTION / Resolution: 1.403 Å

PDB-4y43:
Endothiapepsin in complex with fragment 42
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-4y44:
Endothiapepsin in complex with fragment 164
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-4y45:
Endothiapepsin in complex with fragment 291
Method: X-RAY DIFFRACTION / Resolution: 1.06 Å

PDB-4y47:
Endothiapepsin in complex with fragment 162
Method: X-RAY DIFFRACTION / Resolution: 1.19 Å

PDB-4y4a:
Endothiapepsin in complex with fragment 286
Method: X-RAY DIFFRACTION / Resolution: 1.278 Å

PDB-4y4b:
Endothiapepsin in complex with fragment 323
Method: X-RAY DIFFRACTION / Resolution: 1.108 Å

PDB-4y4e:
Endothiapepsin in complex with fragment 131
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-4y4t:
Endothiapepsin in complex with fragment 114
Method: X-RAY DIFFRACTION / Resolution: 1.301 Å

PDB-4y4u:
Endothiapepsin in complex with fragment 14
Method: X-RAY DIFFRACTION / Resolution: 1.754 Å

PDB-4y4w:
Endothiapepsin in complex with fragment 125
Method: X-RAY DIFFRACTION / Resolution: 1.451 Å

PDB-4y4x:
Endothiapepsin in complex with fragment 51
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-4y4z:
Endothiapepsin in complex with fragment 73
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-4y50:
Endothiapepsin in complex with fragment 81
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-4y51:
Endothiapepsin in complex with fragment 52
Method: X-RAY DIFFRACTION / Resolution: 1.603 Å

PDB-4y53:
Endothiapepsin in complex with fragment 54
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-4y54:
Endothiapepsin in complex with fragment 56
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-4y56:
Endothiapepsin in complex with fragment 58
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-4y57:
Endothiapepsin in complex with fragment 63
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-4y5l:
Endothiapepsin in its apo form
Method: X-RAY DIFFRACTION / Resolution: 0.99 Å

PDB-4y5m:
Endothiapepsin in complex with fragment 328
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-4y5n:
Endothiapepsin in complex with fragment 337
Method: X-RAY DIFFRACTION / Resolution: 1.29 Å

PDB-4y5p:
Endothiapepsin in complex with fragment 338
Method: X-RAY DIFFRACTION / Resolution: 1.229 Å

PDB-4yck:
Endothiapepsin in complex with fragment 211
Method: X-RAY DIFFRACTION / Resolution: 1.07 Å

PDB-4yct:
Endothiapepsin in complex with fragment 216
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-4ycy:
Endothiapepsin in complex with fragment 218
Method: X-RAY DIFFRACTION / Resolution: 1.699 Å

PDB-4yd3:
Endothiapepsin in complex with fragment 224
Method: X-RAY DIFFRACTION / Resolution: 1.248 Å

PDB-4yd4:
Endothiapepsin in complex with fragment 227
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-4yd5:
Endothiapepsin in complex with fragment 236
Method: X-RAY DIFFRACTION / Resolution: 1.209 Å

PDB-4yd6:
Endothiapepsin in complex with fragment 240
Method: X-RAY DIFFRACTION / Resolution: 1.298 Å

PDB-4yd7:
Endothiapepsin in complex with fragment 255
Method: X-RAY DIFFRACTION / Resolution: 1.419 Å

PDB-5dpz:
Endothiapepsin in complex with fragment 31
Method: X-RAY DIFFRACTION / Resolution: 1.328 Å

PDB-5dq1:
Endothiapepsin in complex with fragment 34
Method: X-RAY DIFFRACTION / Resolution: 1.489 Å

PDB-5dq2:
Endothiapepsin in complex with fragment 48
Method: X-RAY DIFFRACTION / Resolution: 1.514 Å

PDB-5dq4:
Endothiapepsin in complex with fragment 66
Method: X-RAY DIFFRACTION / Resolution: 1.15 Å

PDB-5dq5:
Endothiapepsin in complex with fragment 209
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-5dr0:
Endothiapepsin in complex with fragment 203
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-5dr1:
Endothiapepsin in complex with fragment 278
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-5dr3:
Endothiapepsin in complex with fragment 333
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5dr4:
Endothiapepsin in complex with fragment 231
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5dr7:
Endothiapepsin in complex with fragment 311
Method: X-RAY DIFFRACTION / Resolution: 1.234 Å

PDB-5dr8:
Endothiapepsin in complex with fragment 330
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-5hco:
Endothiapepsin in complex with hydrazide
Method: X-RAY DIFFRACTION / Resolution: 1.17 Å

PDB-5is4:
Endothiapepsin in complex with chiral brominated primary amine fragment
Method: X-RAY DIFFRACTION / Resolution: 1.368 Å

PDB-5isj:
Endothiapepsin in complex with chiral chlorinated primary amine fragment
Method: X-RAY DIFFRACTION / Resolution: 1.651 Å

PDB-5isk:
Endothiapepsin in complex with fluorinated primary amine fragment
Method: X-RAY DIFFRACTION / Resolution: 1.14 Å

PDB-5j25:
Endothiapepsin in complex with fragment 158
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

Chemicals

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-F90:
4-chlorobenzyl carbamimidothioate

ChemComp-HOH:
WATER / Water

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-45L:
3-methylbenzohydrazide

ChemComp-45J:
4-chloro-2-methylthieno[2,3-d][1,2,3]diazaborinin-1(2H)-ol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-45M:
4-bromo-N'-(3,4-dihydro-2H-pyrrol-5-yl)benzohydrazide

ChemComp-F05:
1H-isoindol-3-amine

ChemComp-78B:
ethyl 4-(aminomethyl)benzoate

ChemComp-463:
N-[3-(aminomethyl)phenyl]acetamide

ChemComp-45Y:
2-(4-fluorophenyl)acetohydrazide

ChemComp-45V:
2-[(1S)-2-acetyl-1,2-dihydroisoquinolin-1-yl]-N,N-dimethylacetamide

ChemComp-46S:
1-(6-methylpyrimidin-4-yl)azepane

ChemComp-F02:
4-(diethylamino)benzohydrazide

ChemComp-F06:
2-chlorobenzyl carbamimidothioate

ChemComp-46L:
6-(dimethylamino)pyridine-3-carboxylic acid

ChemComp-46Q:
(2R)-2-methyl-2-(morpholin-4-yl)butan-1-amine

ChemComp-46P:
4-methyl-5-(1-methyl-1H-imidazol-2-yl)-1,3-thiazol-2-amine

ChemComp-F41:
N-(1,3-benzodioxol-5-yl)-2-(piperidin-1-yl)acetamide

ChemComp-46O:
(2R)-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidine

ChemComp-46T:
(1E,2E)-N,N'-di(propan-2-yl)cyclohepta-3,5-diene-1,2-diimine

ChemComp-46Y:
4,6-dimethyl-2-{[3-(morpholin-4-yl)propyl]amino}pyridine-3-carbonitrile

ChemComp-F91:
N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine

ChemComp-479:
4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide

ChemComp-47G:
5-(aminomethyl)-2-methoxyphenol

ChemComp-47H:
6,6,8-trimethyl-5,6-dihydro[1,3]dioxolo[4,5-g]quinoline

ChemComp-46R:
N-(2,2,2-trifluoroethyl)-1,2-oxazole-3-carboxamide

ChemComp-46X:
3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile

ChemComp-46V:
1-(4-bromo-2-chlorophenyl)-3-methylthiourea

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-46W:
4-methylpiperidine-1-carboximidamide

ChemComp-47Q:
5-[(pyridin-2-ylmethyl)amino]-1,3-dihydro-2H-benzimidazol-2-one

ChemComp-47R:
(1Z)-N,N-diethylethanimidamide

ChemComp-47S:
3-(dimethylamino)benzohydrazide

ChemComp-47A:
2-amino-1-(4-bromophenyl)ethanone

ChemComp-47B:
3-(3,4-difluorophenyl)imidazo[2,1-c][1,2,4]triazine

ChemComp-47E:
(2R)-(3-chlorophenyl)(hydroxy)ethanoic acid

ChemComp-47J:
1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine

ChemComp-F63:
N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-NA:
Unknown entry

ChemComp-47Y:
3-[(4E)-4-imino-5,6-dimethylfuro[2,3-d]pyrimidin-3(4H)-yl]-N,N-dimethylpropan-1-amine

ChemComp-487:
6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine

ChemComp-483:
2-(1H-imidazol-1-yl)-N-(trans-4-methylcyclohexyl)acetamide

ChemComp-FBF:
4-(trifluoromethyl)benzenecarboximidamide

ChemComp-4AO:
2-(4-ethoxy-8-methylquinazolin-2-yl)guanidine

ChemComp-4AQ:
2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-4AY:
4-(bromomethyl)benzoic acid

ChemComp-BR:
BROMIDE ION / Bromide

ChemComp-4AV:
1-(2-chloro-5-nitrophenyl)-N-methylmethanamine

ChemComp-4AS:
N-methyl-1-(1-methyl-1H-imidazol-2-yl)methanamine

ChemComp-F5N:
2-(imidazo[1,2-a]pyridin-2-yl)-N-phenylacetamide

ChemComp-51V:
2-methylaniline / O-Toluidine

ChemComp-5HL:
3-[(cyclopropylamino)methyl]-8-ethylquinolin-2(1H)-one

ChemComp-5HO:
N-(5-chloropyridin-2-yl)-2-oxo-2-(pyrrolidin-1-yl)acetamide

ChemComp-5HQ:
1-[6-(furan-2-yl)pyridin-3-yl]methanamine

ChemComp-5HS:
3-[2-(4-methyl-1,2-oxazol-3-yl)ethyl]pyridine

ChemComp-5GC:
5-(methylsulfanyl)-4-(propan-2-ylsulfonyl)-1H-pyrazol-3-amine

ChemComp-5GJ:
[(3R)-3-hydroxypiperidin-1-yl](1-phenylcyclopropyl)methanone

ChemComp-5GL:
4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one

ChemComp-5GQ:
7-methyl-3,4-dihydro-2~{H}-pyrido[1,2-a]pyrimidin-3-ol

ChemComp-5HJ:
(2R)-3-cyclopropyl-2-(4-methoxyphenyl)-1,3-thiazolidin-4-one

ChemComp-5G1:
2-chlorobenzohydrazide

ChemComp-601:
4-(dimethylamino)benzohydrazide

ChemComp-6LY:
(1S)-2-amino-1-(4-bromophenyl)ethan-1-ol

ChemComp-6LE:
(1S)-2-amino-1-(4-chlorophenyl)ethan-1-ol

ChemComp-6LZ:
2-amino-1-(4-fluorophenyl)ethan-1-one

ChemComp-47K:
2-(4-methylpiperidin-1-yl)-N-[3-(propan-2-yl)-1,2-oxazol-5-yl]acetamide

Source
  • cryphonectria parasitica (chestnut blight fungus)
KeywordsHYDROLASE / fagment screening / inhibition / fragment screening / aspartic protease

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more