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Structure paper

TitleEnhanced identification of small molecules binding to hnRNP A1 via in silico hotspot and cryptic pockets mapping coupled with X-Ray fragment screening
Journal, issue, pagesTo Be Published
Publish dateApr 27, 2024 (structure data deposition date)
AuthorsDunnett, L. / Prischi, F.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.39 - 1.8 Å
Structure data

PDB-9f4d:
UP1 in complex with Z1203107138
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9f4e:
UP1 in complex with Z1152242726
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-9f4f:
UP1 in complex with Z86417414
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4g:
UP1 in complex with Z1373445602
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4h:
UP1 in complex with Z106579662
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4j:
UP1 in complex with Z416341642
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4k:
UP1 in complex with ZINC72259689
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-9f4l:
UP1 in complex with Z104584152
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4m:
UP1 in complex with Z1401276297
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9f4n:
UP1 in complex with Z137811222
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4o:
UP1 in complex with Z991506900
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4p:
UP1 in complex with Z1217960891
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4q:
UP1 in complex with Z641239276
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4r:
UP1 in complex with Z802821712
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-9f4s:
UP1 in complex with Z56880342
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4t:
UP1 in complex with EN300-805013
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-9f4u:
UP1 in complex with Z111529496
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4v:
UP1 in complex with EN300-118084
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4w:
UP1 in complex with Z54508609
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9f4x:
UP1 in complex with Z1220452176
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9f4y:
UP1 in complex with Z90120418
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f4z:
UP1 in complex with Z57040482
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9f50:
UP1 in complex with Z906021418
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9f51:
UP1 in complex with Z608065044
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9f52:
UP1 in complex with Z734147462
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9f53:
UP1 in complex with Z237527902
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-9f54:
UP1 in complex with EN300-197154
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-9f55:
UP1 in complex with Z235361315
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-9f5c:
UP1 in complex with Z198195770
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9f5d:
UP1 in complex with Z641230552
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9f5e:
UP1 in complex with Z30820160
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9f5f:
UP1 in complex with Z992569480
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9f5g:
UP1 in complex with EN300-115958
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-9f5k:
UP1 in complex with Z33546965
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-9f7f:
UP1 in complex with Z1491353358
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-9f7h:
UP1 in complex with Z45617795
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

Chemicals

ChemComp-JH1:
1-ethyl-N-[(4-fluorophenyl)methyl]-1H-pyrazole-4-carboxamide

ChemComp-HOH:
WATER

ChemComp-VZM:
N-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea

PDB-1h9t:
FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR

ChemComp-SZE:
4-(3-fluoranylpyridin-2-yl)-1-methyl-piperazin-2-one

ChemComp-NUY:
[4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone

ChemComp-NWP:
(2R)-N,2-dimethyl-N-(propan-2-yl)morpholine-4-sulfonamide

PDB-1h9r:
Tungstate bound complex Dimop domain of ModE from E.coli

ChemComp-WGP:
N,N-dimethyl-N~2~-phenylglycinamide

PDB-1h97:
Trematode hemoglobin from Paramphistomum epiclitum

ChemComp-O3J:
1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one

PDB-1h95:
Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures)

ChemComp-Q49:
(3S)-3-(3-fluorophenoxy)-1-methylpyrrolidin-2-one

PDB-1h9s:
Molybdate bound complex of Dimop domain of ModE from E.coli

ChemComp-K3J:
N-ethyl-6-methylpyridazin-3-amine

ChemComp-JGA:
N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea

ChemComp-WZY:
N-(4-methoxyphenyl)glycinamide

ChemComp-LXA:
~{N}-(1~{H}-benzimidazol-2-ylmethyl)-2-methoxy-ethanamide

ChemComp-UQJ:
3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide

ChemComp-O0M:
1-{[4-(propan-2-yl)phenyl]methyl}piperidin-4-ol

ChemComp-HWH:
~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide

ChemComp-W0S:
1-(3,4,5-trimethoxyphenyl)methanamine

ChemComp-9KS:
N-(2-hydroxyphenyl)acetamide

ChemComp-K2G:
5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide

PDB-1h9v:
Human Fc-gamma-Receptor IIa (FcgRIIa), monoclinic

PDB-1h9w:
Native Dioclea Guianensis seed lectin

ChemComp-K3A:
N-(5-methyl-1H-pyrazol-3-yl)acetamide

ChemComp-K3Y:
1-methyl-3-[(3R)-piperidin-3-yl]-1H-pyrazole-4-carboxamide

PDB-1h9u:
The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268

ChemComp-LJA:
N-[3-(carbamoylamino)phenyl]acetamide

PDB-1h9x:
Cytochrome cd1 Nitrite Reductase, reduced form

ChemComp-JFP:
N-(4-methyl-1,3-thiazol-2-yl)propanamide

ChemComp-W0J:
(3R)-N-methyl-1-(pyridazin-3-yl)piperidin-3-amine

ChemComp-Z9I:
1-[(2R)-1-(methanesulfonyl)pyrrolidin-2-yl]methanamine

ChemComp-ONQ:
~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide

ChemComp-WNM:
(3S)-1-(phenylsulfonyl)pyrrolidin-3-amine

ChemComp-JFM:
N-(2-phenylethyl)methanesulfonamide

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / fragment screening / hnRNP A1 / UP1 / RNA/DNA BINDING PROTEIN / UP1-fragment complex

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