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Structure paper

TitleRational fragment-based design of compounds targeting the PWWP domain of the HRP family.
Journal, issue, pagesEur. J. Med. Chem., Vol. 280, Page 116960-116960, Year 2024
Publish dateAug 29, 2024 (structure data deposition date)
AuthorsVantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. ...Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / Veverka, V. / Verwilst, P. / Van Aerschot, A. / Debyser, Z. / Strelkov, S.V.
External linksEur. J. Med. Chem. / PubMed:39461037
MethodsX-ray diffraction
Resolution1.41 - 2.11 Å
Structure data

PDB-7hg0:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z46169212
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-7hg1:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1079512010
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-7hg2:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1401276297
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7hg3:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z319891284
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7hg4:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1696844792
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hg5:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z2142244288
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hg6:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z839706072
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7hg7:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z46169164
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7hg8:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z445856640
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7hg9:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z131516158
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-7hga:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1980894300
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hgb:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z33297786
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7hgc:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1428159350
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-7hgd:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z363071686
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7hge:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z45527714
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7hgf:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1262433643
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7hgg:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z422396686
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7hgh:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z26823525
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-7hgi:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z57475068
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7hgj:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z751811134
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7hgk:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z31721798
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7hgl:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z137790394
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7hgm:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z438067480
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7hgn:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z54226006
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7hgo:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z431807512
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-7hgp:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z19735067
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-7hgq:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z94597856
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7hgr:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z104924088
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-7hgs:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z355202286
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-7hgt:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z354992234
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hgu:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z216450634
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7hgv:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z103740620
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-7hgw:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1407673036
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7hgx:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1362754425
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hgy:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7hgz:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1509882419
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7hh0:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z57390007
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7hh1:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z53825177
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-7hh2:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1238477757
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hh3:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1245580425
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7hh4:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1139246057
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-7hh5:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z168883358
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7hh6:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z54633859
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7hh7:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1003207278
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7hh8:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1258992717
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-7hh9:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1250132788
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7hha:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z53825020
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7hhb:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1263529721
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hhc:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z31432964
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7hhd:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z90526999
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7hhe:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1203252645
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7hhf:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1267773633
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7hhg:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1741966151
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7hhh:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1259335862
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7hhi:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z805551440
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-7hhj:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z100642432
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hhk:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1247413608
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7hhl:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1262327517
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7hhm:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z234898257
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hhn:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z133632670
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7hho:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z235361315
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7hhp:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z31723394
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7hhq:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1741815708
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7hhr:
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z57744712
Method: X-RAY DIFFRACTION / Resolution: 2.03 Å

PDB-9g91:
Crystal structure of HRP-2 PWWP domain in complex with compound 43
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-9g94:
Crystal structure of HRP-2 PWWP domain in complex with compound 32
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-9g96:
Crystal structure of HRP-2 PWWP domain in complex with compound 42
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-9grs:
Crystal structure of HRP-2 PWWP domain in complex with compound 8
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-9grt:
Crystal structure of HRP-2 PWWP domain in complex with compound 29
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-9gru:
Crystal structure of HRP-2 PWWP domain in complex with compound 30
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-9grv:
Crystal structure of HRP-2 PWWP domain in complex with compound 37
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

PDB-1a3p:
ROLE OF THE 6-20 DISULFIDE BRIDGE IN THE STRUCTURE AND ACTIVITY OF EPIDERMAL GROWTH FACTOR, NMR, 20 STRUCTURES

ChemComp-HOH:
WATER

ChemComp-UWS:
6-methyl-2-[(3-methyl-1,2-oxazol-5-yl)methyl]pyridazin-3(2H)-one

PDB-1h97:
Trematode hemoglobin from Paramphistomum epiclitum

ChemComp-U0S:
(5S)-7-(pyrazin-2-yl)-2-oxa-7-azaspiro[4.4]nonane

ChemComp-ZQD:
3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol

ChemComp-WV4:
N-ethyl-2-fluoro-4-(methylsulfonyl)aniline

ChemComp-2NU:
2-(4-bromanylpyrazol-1-yl)-~{N}-cyclopropyl-~{N}-methyl-ethanamide

ChemComp-EJQ:
~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide

ChemComp-VZP:
N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea

PDB-1a3q:
HUMAN NF-KAPPA-B P52 BOUND TO DNA

ChemComp-TU6:
[4-methyl-6-(piperidin-1-yl)pyrimidin-2-yl]methanol

PDB-1a34:
SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX

PDB-1aj5:
CALPAIN DOMAIN VI APO

PDB-1a3s:
HUMAN UBC9

ChemComp-X0S:
2-chloro-N-methylbenzene-1-sulfonamide

ChemComp-T0Y:
1-[(thiophen-3-yl)methyl]piperidin-4-ol

PDB-1a4b:
AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS

PDB-1a4a:
AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT 16 DEGREES CELSIUS

PDB-1a35:
HUMAN TOPOISOMERASE I/DNA COMPLEX

ChemComp-ZUG:
N,N-dimethylpyridine-3-sulfonamide

ChemComp-NW4:
3-cyclohexyl-1-(morpholin-4-yl)propan-1-one

ChemComp-WJ4:
4-[(5-chloro-1,2,3-thiadiazol-4-yl)methyl]morpholine

PDB-1am1:
ATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE

ChemComp-NX7:
(2,6-difluorophenyl)(pyrrolidin-1-yl)methanone

ChemComp-8DH:
N-methyl-3-oxo-N-(propan-2-yl)piperazine-1-sulfonamide

ChemComp-I8G:
2-(4-fluorophenoxy)-1-(pyrrolidin-1-yl)ethan-1-one

ChemComp-K2S:
N,N,3,5-tetramethyl-1H-pyrazole-4-sulfonamide

PDB-1am6:
CARBONIC ANHYDRASE II INHIBITOR: ACETOHYDROXAMATE

PDB-1amx:
COLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN

PDB-1a3r:
FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170)

ChemComp-VVJ:
N-cycloheptyl-N-methylmethanesulfonamide

PDB-1a33:
PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI

PDB-1a32:
RIBOSOMAL PROTEIN S15 FROM BACILLUS STEAROTHERMOPHILUS

PDB-1a31:
HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-NYV:
1-(propan-2-yl)-1H-imidazole-4-sulfonamide

ChemComp-RYP:
~{N}-methyl-1-pyridin-4-yl-methanamine

ChemComp-VVG:
N-(2-fluorophenyl)ethanesulfonamide

PDB-1akb:
STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE

PDB-1a3x:
PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+

PDB-1a39:
HUMICOLA INSOLENS ENDOCELLULASE EGI S37W, P39W DOUBLE-MUTANT

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

ChemComp-WO7:
1-(1,4-diazepan-1-yl)ethan-1-one

ChemComp-UUY:
2-[methyl(pyridin-2-yl)amino]ethan-1-ol

ChemComp-LJR:
1-cyclohexyl-N-methylmethanesulfonamide


ChemComp, No image

ChemComp-KF8:
Unknown entry

PDB-1a3w:
PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+

ChemComp-TE0:
1-(ethanesulfonyl)piperidine-4-carboxylic acid

PDB-1a3u:
STAPHYLOCOCCAL NUCLEASE, CYCLOHEXANE THIOL DISULFIDE TO V23C VARIANT

ChemComp-SYX:
(4-methylpiperazin-1-yl)[(2R)-oxolan-2-yl]methanone

PDB-1a3v:
STAPHYLOCOCCAL NUCLEASE, CYCLOPENTANE THIOL DISULFIDE TO V23C VARIANT

PDB-1a38:
14-3-3 PROTEIN ZETA BOUND TO R18 PEPTIDE

PDB-1a36:
TOPOISOMERASE I/DNA COMPLEX

ChemComp-W1A:
N-[(piperidin-4-yl)methyl]methanesulfonamide

PDB-1a3t:
STAPHYLOCOCCAL NUCLEASE, V23C VARIANT, COMPLEX WITH 2-FLUOROETHANE THIOL AND 3',5'-THYMIDINE DIPHOSPHATE

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

ChemComp-WJ7:
2-bromo-4-fluoro-N,N-dimethylbenzamide

ChemComp-LPU:
1-(methanesulfonyl)piperidin-4-ol

PDB-1a37:
14-3-3 PROTEIN ZETA BOUND TO PS-RAF259 PEPTIDE

ChemComp-UWD:
N-methyl-1-([1,2,4]triazolo[4,3-a]pyridin-3-yl)methanamine

PDB-1a30:
HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR

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

PDB-1a3z:
REDUCED RUSTICYANIN AT 1.9 ANGSTROMS

PDB-1a3y:
ODORANT BINDING PROTEIN FROM NASAL MUCOSA OF PIG

ChemComp-YEB:
N,N-dimethylmorpholine-4-sulfonamide

PDB-1ii3:
Structure of S. nuclease quintuple mutant V23I/V66L/I72L/I92L/V99L

PDB-1d73:
Unknown entry

PDB-1ii2:
Crystal Structure of Phosphoenolpyruvate Carboxykinase (PEPCK) from Trypanosoma cruzi

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

PDB-1h6y:
The role of conserved amino acids in the cleft of the C-terminal family 22 carbohydrate binding module of Clostridium thermocellum Xyn10B in ligand binding

ChemComp-BYZ:
4-bromo-1H-pyrazole

ChemComp-PYZ:
4-IODOPYRAZOLE

ChemComp-HHN:
5-bromanylpyrimidine

Source
  • homo sapiens (human)
KeywordsGENE REGULATION / Inhibitor / Fragment screening / Epigenetic reader / methyllysine / PWWP / Diamond Light Source / I04-1 / PanDDA / XChem

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