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Structure paper

TitleCrystallographic fragment screening supports tool compound discovery and reveals conformational flexibility in human deoxyhypusine synthase
Journal, issue, pagesTo Be Published
Publish dateFeb 15, 2025 (structure data deposition date)
AuthorsWilk, P. / Wator-Wilk, E. / Muszak, D. / Kochanowski, P. / Krojer, T. / Grudnik, P.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.27 - 1.95 Å
Structure data

PDB-9id1:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00015
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-9id2:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00019
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9id3:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligandT00025
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9id4:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00038
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9id5:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00048
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9id6:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00049
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-9id7:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00058
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9id8:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00065 covalently linked to the catalytic lysine (K329)
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-9id9:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00068
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9ida:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00079
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-9idb:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00082
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9idc:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00086
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-9idd:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00089
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9ide:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00096
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-9idf:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00127
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-9idg:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00128
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9idh:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00143
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-9idi:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00154
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-9idj:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00155
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9idk:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00165
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-9idl:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00173
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9idm:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00175
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-9idn:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00178
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-9ido:
Human Deoxyhypusine Synthase Fragment Screening Campaign - UNLand VT00188
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9idp:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00190
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-9idq:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00193
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9idr:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00204
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-9ids:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00210
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-9idt:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00213
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

PDB-9idu:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00215
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-9idv:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00216
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

PDB-9idw:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00217
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-9idx:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00218
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-9idy:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00219
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-9idz:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00221
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-9ie0:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00222
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-9ie1:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00223
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-9ie2:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00224
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9ie3:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00228
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-9ie4:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00229
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-9ie5:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00230
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-9ie6:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00234
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-9ie7:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00236
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-9ie8:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00253
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-9ie9:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00254
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9iea:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00257
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-9ieb:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00259
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-9iec:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00261
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9ied:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00268
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-9iee:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00403
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-9ief:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00405
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9ieg:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00407
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-9ieh:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00409
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-9iei:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00416
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-9iej:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00417
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-9iek:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00423
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-9iel:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00424
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-9iem:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00427
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-9ien:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00428
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-9ieo:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00438
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-9iep:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00440
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-9ieq:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00441
Method: X-RAY DIFFRACTION / Resolution: 1.41 Å

PDB-9ier:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00442
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-9ies:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00445
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9iet:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00446
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-9ieu:
Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00447
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-9iex:
Human Deoxyhypusine Synthase Fragment Screening Campaign - VT0155 follow-up ligand DMP7
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM


PDB Unreleased entry

PDB-1i28: CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-ASPARTATE

ChemComp-MRD:
(4R)-2-METHYLPENTANE-2,4-DIOL / precipitant*YM

ChemComp-HOH:
WATER

PDB-1igq:
C-terminal Domain of Transcriptional Repressor Protein KorB

ChemComp-EDO:
1,2-ETHANEDIOL

PDB-1igp:
X-RAY CRYSTALLOGRAPHIC STUDIES OF RECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI

PDB-1i2a:
CRYSTAL STRUCTURE OF L1 RIBOSOMAL PROTEIN FROM METHANOCOCCUS JANNASCHII WITH 1.85A RESOLUTION.

PDB-1i14:
ANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-GLUTAMIC ACID MUTANT

PDB-1i20:
MUTANT HUMAN LYSOZYME (A92D)

PDB-1i13:
ANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-ALANINE MUTANT

PDB-1i3p:
THE 3.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE

PDB-1i2z:
E. COLI ENOYL REDUCTASE IN COMPLEX WITH NAD AND BRL-12654

ChemComp-UYY:
2-methoxybenzamide

PDB-1i3d:
HUMAN CARBONMONOXY HEMOGLOBIN BART'S (GAMMA4)

PDB-1i17:
NMR STRUCTURE OF MOUSE DOPPEL 51-157

PDB-1i2d:
CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM

PDB-1i2f:
Ribonuclease T1 V16A mutant, form II

PDB-1i2o:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT E96A

PDB-1i22:
MUTANT HUMAN LYSOZYME (A83K/Q86D/A92D)

ChemComp-9NN:
4-(aminomethyl)pyridin-2-amine

PDB-1i2s:
BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3

ChemComp-PYQ:
PYROQUILON

PDB-1i29:
CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE

PDB-1i2m:
RAN-RCC1-SO4 COMPLEX

ChemComp-OCH:
QUINOLIN-2(1H)-ONE

PDB-1i3a:
RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE

PDB-1i2r:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT S176A

PDB-1i11:
SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE

PDB-1i2l:
DEOXYCHORISMATE LYASE FROM ESCHERICHIA COLI WITH INHIBITOR

PDB-1i19:
CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM B.STEROLICUM

PDB-1i3m:
MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE

PDB-1i2w:
BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 COMPLEXED WITH CEFOXITIN

PDB-1i2t:
X-RAY STRUCTURE OF THE HUMAN HYPERPLASTIC DISCS PROTEIN: AN ORTHOLOG OF THE C-TERMINAL DOMAIN OF POLY(A)-BINDING PROTEIN

PDB-1igm:
THREE DIMENSIONAL STRUCTURE OF AN FV FROM A HUMAN IGM IMMUNOGLOBULIN

PDB-1i3e:
HUMAN AZIDO-MET HEMOGLOBIN BART'S (GAMMA4)

PDB-1igj:
26-10 FAB:DIGOXIN COMPLEX-AFFINITY AND SPECIFICITY DUE TO SURFACE COMPLEMENTARITY

PDB-1ign:
DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE

ChemComp-2AQ:
QUINOLIN-2-AMINE

PDB-1i3c:
RESPONSE REGULATOR FOR CYANOBACTERIAL PHYTOCHROME, RCP1

PDB-1i2g:
Ribonuclease T1 V16T mutant

ChemComp-X4P:
2-chloropyridine-4-carboxamide

PDB-1i3k:
MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE

PDB-1i3j:
CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE

PDB-1i10:
HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE


PDB Unreleased entry

PDB-1i23: X-RAY STRUCTURE OF A PHOSPHOSERYL INTERMEDIATE OF AN IMPROVED MUTANT OF E. COLI ALKALINE PHOSPHATASE

PDB-1i27:
CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 SUBUNIT OF HUMAN TRANSCRIPTION FACTOR IIF (TFIIF)

PDB-1i3r:
CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE

PDB-1i3l:
MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE

PDB-1i2p:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT D17A

ChemComp-VSL:
methyl 4,5,6,7-tetrahydro-2H-indazole-3-carboxylate

PDB-1i2n:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT N35A

PDB-1i25:
Three dimensional solution structure of huwentoxin-II by 2D 1H-NMR

PDB-1i24:
HIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD-TYPE PROTEIN SQD1, WITH NAD AND UDP-GLUCOSE

ChemComp-L3N:
1~{H}-quinazoline-2,4-dione

PDB-1i3g:
CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE

PDB-1i3f:
Ribonuclease T1 V89S mutant

PDB-1i3h:
CONCANAVALIN A-DIMANNOSE STRUCTURE

PDB-1i2x:
2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM

PDB-1i3n:
MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE

PDB-1i21:
CRYSTAL STRUCTURE OF YEAST GNA1

PDB-1ed2:
Unknown entry

PDB-1i2e:
Ribonuclease T1 V16A mutant, form I

PDB-1i3i:
Ribonuclease T1 V78T mutant

ChemComp-DH6:
CINNAMIDE

PDB-1i3o:
CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP-BIR2 AND CASPASE 3

PDB-1i3t:
MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATT(MO4)CGCG): THE WATSON-CRICK TYPE AND WOBBLE N4-METHOXYCYTIDINE/GUANOSINE BASE PAIRS IN B-DNA

PDB-1i12:
CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA

PDB-1i3s:
THE 2.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A MUTATED BACULOVIRUS P35 AFTER CASPASE CLEAVAGE

PDB-1i3b:
Unknown entry

PDB-1i7e:
C-Terminal Domain Of Mouse Brain Tubby Protein bound to Phosphatidylinositol 4,5-bis-phosphate

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / fragment screening / polyamines / high-throughput / posttranslational modifications / posttranslational modifications' / TRANSCRIPTION

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