PDB-9iex: Human Deoxyhypusine Synthase Fragment Screening Campaign - VT0155...

ID or keywords:

Entry

Database: PDB / ID: 9iex

Title

Human Deoxyhypusine Synthase Fragment Screening Campaign - VT0155 follow-up ligand DMP7

Components

(Deoxyhypusine synthase) x 2

Keywords

TRANSFERASE / fragment screening / polyamines / high-throughput / posttranslational modifications

Function / homology

Function and homology information

peptidyl-hypusine biosynthetic process / deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Wilk, P. / Wator-Wilk, E. / Grudnik, P.

Funding support

Poland, 2items

Citation

Journal: To Be Published
Title: Crystallographic fragment screening supports tool compound discovery and reveals conformational flexibility in human deoxyhypusine synthase
Authors: Wilk, P. / Wator-Wilk, E. / Muszak, D. / Kochanowski, P. / Krojer, T. / Grudnik, P.

History

Deposition	Feb 15, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 21, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9iex.cif.gz	542.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9iex.ent.gz		Display	PDB format
PDBx/mmJSON format	9iex.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ie/9iex ftp://data.pdbj.org/pub/pdb/validation_reports/ie/9iex	HTTPS FTP

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Related structure data

Related structure data	9id1C 9id2C 9id3C 9id4C 9id5C 9id6C 9id7C 9id8C 9id9C 9idaC 9idbC 9idcC 9iddC 9ideC 9idfC 9idgC 9idhC 9idiC 9idjC 9idkC 9idlC 9idmC 9idnC 9idoC 9idpC 9idqC 9idrC 9idsC 9idtC 9iduC 9idvC 9idwC 9idxC 9idyC 9idzC 9ie0C 9ie1C 9ie2C 9ie3C 9ie4C 9ie5C 9ie6C 9ie7C 9ie8C 9ie9C 9ieaC 9iebC 9iecC 9iedC 9ieeC 9iefC 9iegC 9iehC 9ieiC 9iejC 9iekC 9ielC 9iemC 9ienC 9ieoC 9iepC 9ieqC 9ierC 9iesC 9ietC 9ieuC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

Similarity search - Function & homology

F&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Deoxyhypusine synthase

B: Deoxyhypusine synthase

C: Deoxyhypusine synthase

D: Deoxyhypusine synthase

hetero molecules

177 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: homology

Unit cell

Length a, b, c (Å)	104.318, 104.318, 159.679
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Deoxyhypusine synthase / DHS Mass: 44154.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase
#2: Protein	Deoxyhypusine synthase / DHS Mass: 44136.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase
#3: Chemical	ChemComp-A1I7E / 6-[2-oxidanylidene-2-(11-oxidanylidene-1-azatricyclo[6.3.1.0^{4,12}]dodeca-4(12),5,7-trien-6-yl)ethyl]-1-azatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-one Mass: 386.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₂₂N₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 1000, PEG 3350), 100 mM Tris-Bicine pH = 8.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.9793 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2021

Radiation

Monochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.95→49.58 Å / Num. obs: 141429 / % possible obs: 99.8 % / Redundancy: 5.75 % / CC_1/2: 0.995 / R_merge(I) obs: 0.207 / R_rim(I) all: 0.229 / Net I/σ(I): 10.34

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Mean I/σ(I) obs	% possible all
1.95-2.07		2.158	22844	0.626	2.383
2.07-2.21		1.301	21515	0.831	1.435
2.21-2.39		0.885	19941	0.93	0.974
2.39-2.61		0.656	18437	0.944	0.725
2.61-2.92		0.504	16641	0.966	0.555
2.92-3.37		0.34	14678	0.984	0.375
3.37-4.13		0.164	12426	0.989	0.181
4.13-5.81		0.091	9618	0.995	0.101
5.81-49.58	6.19	0.065	5329	0.997	0.072	0.97	99.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→49.58 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1972	2099	1.49 %
R_work	0.1745	-	-
obs	0.1748	141310	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→49.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10168	0	58	551	10777

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	9.656	1517
X-RAY DIFFRACTION	f_chiral_restr	0.067	1591
X-RAY DIFFRACTION	f_plane_restr	0.008	1882

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2	0.4198	138	0.3851	9250	X-RAY DIFFRACTION	99
2-2.05	0.3329	141	0.3196	9331	X-RAY DIFFRACTION	99
2.05-2.1	0.3041	139	0.2868	9209	X-RAY DIFFRACTION	99
2.1-2.16	0.2594	139	0.2594	9232	X-RAY DIFFRACTION	100
2.16-2.23	0.3264	141	0.2446	9312	X-RAY DIFFRACTION	100
2.23-2.31	0.2773	140	0.2137	9264	X-RAY DIFFRACTION	100
2.31-2.4	0.2419	139	0.1947	9259	X-RAY DIFFRACTION	100
2.4-2.51	0.1917	140	0.1717	9305	X-RAY DIFFRACTION	100
2.51-2.65	0.2064	140	0.1687	9268	X-RAY DIFFRACTION	100
2.65-2.81	0.1775	141	0.166	9305	X-RAY DIFFRACTION	100
2.81-3.03	0.2036	140	0.1585	9299	X-RAY DIFFRACTION	100
3.03-3.33	0.1534	140	0.1549	9283	X-RAY DIFFRACTION	100
3.33-3.82	0.1978	140	0.1462	9328	X-RAY DIFFRACTION	100
3.82-4.81	0.1598	140	0.1413	9278	X-RAY DIFFRACTION	100
4.81-49.58	0.177	141	0.1764	9288	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.8795	-0.366	-0.4508	1.4098	-0.4672	2.8858	0.0874	0.1774	0.2632	-0.3383	-0.091	-0.2015	-0.4888	0.0679	-0.0197	0.7202	0.0361	0.0404	0.2307	0.0151	0.4305	-29.2277	43.6579	-14.3793
2	1.0121	-0.4108	-0.1821	1.1958	0.4783	1.3132	0.2493	0.2248	-0.0847	-0.3582	-0.2093	-0.0416	-0.0181	0.0578	-0.0382	0.562	0.1197	-0.0315	0.3692	0.0046	0.3113	-20.9133	17.1772	-26.8134
3	2.9712	0.4275	0.3245	1.8393	0.1612	2.0009	0.1559	0.0765	0.2742	-0.1489	-0.1187	-0.1839	-0.4176	0.3307	-0.0226	0.5591	-0.0018	0.08	0.3104	0.0429	0.3555	-17.8748	36.0357	-14.7332
4	1.8682	-0.0337	0.2923	1.8216	0.1398	2.0465	0.0643	-0.0895	-0.3011	-0.1865	0.0772	-0.0488	0.4835	0.2555	-0.1336	0.3526	0.0394	-0.0388	0.3789	0.0345	0.3328	-5.5518	3.7212	3.1723
5	1.3674	0.107	0.1237	1.0381	-0.0508	1.8423	0.1305	0.1641	0.0855	-0.2383	-0.1023	-0.133	-0.0228	0.4592	-0.0177	0.388	0.0242	0.0309	0.4778	0.0268	0.3403	-1.2198	16.6732	-11.8207
6	1.0454	-1.3028	0.1538	2.1688	-0.1362	2.097	0.0289	-0.0893	0.1644	0.0508	-0.0277	-0.3775	-0.1344	0.7462	-0.0607	0.3157	-0.1231	0.0186	0.7065	-0.0141	0.4302	6.2314	19.4809	7.3873
7	1.8878	-0.3493	0.5539	3.2806	0.9891	4.4942	-0.0147	-0.7648	0.2592	0.466	0.0045	-0.0923	-0.8776	0.4005	-0.0436	0.4547	-0.2024	0.0047	0.78	-0.0976	0.4615	-4.3297	32.3692	25.0388
8	1.5325	-0.0688	-0.2243	1.0075	0.0331	1.5629	-0.0745	-0.4906	-0.0664	0.0384	0.0829	0.1083	-0.0077	-0.0166	-0.0142	0.3096	-0.0222	-0.0169	0.6172	0.0393	0.3199	-25.2734	18.4626	28.7324
9	2.508	0.234	-0.965	1.169	-0.1449	2.1568	0.0956	-0.2775	0.2063	0.1251	0.1358	0.131	-0.2761	0.0019	-0.1491	0.4	0.0278	0.0107	0.638	-0.0517	0.3253	-33.3198	29.8675	33.0317
10	2.0155	-0.0676	0.1402	2.6646	-0.8396	1.9192	0.0135	-0.2361	0.4657	-0.0325	-0.0412	0.0097	-0.5812	-0.0636	-0.0476	0.4754	-0.0789	0.0059	0.4791	-0.0866	0.4204	-14.8028	36.4248	15.4133
11	1.8985	-0.0872	-0.2121	4.1618	-0.2156	2.0011	0.0202	-0.7087	-0.0561	0.2787	0.176	-0.6629	-0.0899	0.627	0.0204	0.2765	-0.0567	-0.0299	0.7425	-0.068	0.3912	-3.8212	21.3775	23.6316
12	1.6936	-0.0306	0.1603	1.6685	-0.3326	1.4322	0.1966	-0.124	-0.1109	-0.0309	-0.0602	0.2735	0.0025	-0.503	-0.145	0.3589	0.0337	-0.0413	0.423	0.0125	0.3584	-46.1149	27.2286	-0.2223
13	1.1702	0.0035	0.1609	1.2259	-0.0288	1.9422	-0.0006	-0.3188	0.1562	0.0713	0.0245	-0.014	-0.4058	-0.2016	-0.0239	0.4271	0.0503	-0.0054	0.4195	-0.0358	0.3263	-36.9779	37.5042	14.6456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 97 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 98 through 271 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 272 through 363 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 28 through 110 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 111 through 363 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 28 through 53 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 54 through 97 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 98 through 239 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 240 through 271 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 272 through 342 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 343 through 363 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 28 through 110 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 111 through 363 )

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