PDB-5o43: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi...

Basic information

• Entry: Database: PDB / ID: 5o43
• Title: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal 2,6-pyridinketone inhibitor.
• Components: 17-beta-hydroxysteroid dehydrogenase 14
• Keywords: OXIDOREDUCTASE / non-steroidal inhibitor / 17beta-HSD14 / 2 / 6-pyridinketone inhibitors

Function / homology

Function:

D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol

Domain/homology:

Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Chem-9JQ / beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
• Authors: Bertoletti, N. / Heine, A. / Braun, F. / Klebe, G. / Marchais-Oberwinkler, S.

Funding support

Germany, 2items

Organization	Grant number	Country
German Research Foundation	MA-5287/1-1	Germany
German Research Foundation	KL-1204/15-1	Germany

• Citation: Journal: Eur J Med Chem / Year: 2018; Title: Structure-based design and profiling of novel 17 beta-HSD14 inhibitors.; Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Frotscher, M. / Guragossian, N. / Madeira Girio, P.A. / Le Borgne, M. / Ettouati, L. / Falson, P. / Muller, S. / Vollmer, G. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.

History

Deposition	May 25, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

Summary:

• 29.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	29,878	5
Polymers	28,683	1
Non-polymers	1,195	4
Water	3,963	220

1

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14

hetero molecules

Summary:

• defined by author&software
• Evidence: mass spectrometry, native mass spectromety and calculation with PISA server
• 120 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	119,510	20
Polymers	114,731	4
Non-polymers	4,780	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_545	-x,-y-1,z	1
crystal symmetry operation	5_555	-x,y,-z	1
crystal symmetry operation	6_545	x,-y-1,-z	1

Calculated values:

Buried area	19810 Å2
ΔGint	-188 kcal/mol
Surface area	32500 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	91.572, 91.572, 133.090
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-476- HOH
2	1	A-589- HOH
3	1	A-619- HOH

Components

Protein / Sugars , 2 types, 2 molecules A

#1: Protein

A 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1

Details:

Mass: 28682.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

#4: Sugar

A-303 ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Details:

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

Identifier:

Identifier	Type	Program
DGlcpb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
b-D-glucopyranose	COMMON NAME	GMML 1.0
b-D-Glcp	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Glc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Non-polymers , 4 types, 223 molecules

#2: Chemical

A-301 ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

#3: Chemical

A-302 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Details:

Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

#5: Chemical

A-304 ChemComp-9JQ / 2-fluoranyl-3-[6-[(4-fluoranyl-3-oxidanyl-phenyl)-methyl-amino]pyridin-2-yl]phenol

Details:

Mass: 328.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₁₄F₂N₂O₂

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.43 ų/Da / Density % sol: 49.42 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 6000 20% Hepes 0.1M DMSO 5% / PH range: 7-8

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9184 Å / Relative weight: 1
• Reflection: Resolution: 1.5→50 Å / Num. obs: 45487 / % possible obs: 99.9 % / Redundancy: 8.53 % / R_sym value: 0.09 / Net I/σ(I): 13.67
• Reflection shell: Resolution: 1.5→1.59 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 7233 / CC_1/2: 0.938 / R_sym value: 0.504 / % possible all: 100

Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4

Resolution: 1.5→50 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.49

	Rfactor	Num. reflection	% reflection
Rfree	0.1674	2275	5 %
Rwork	0.1511	-	-
obs	0.1519	45476	99.89 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1828	0	81	220	2129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1989
X-RAY DIFFRACTION	f_angle_d	0.981	2728
X-RAY DIFFRACTION	f_dihedral_angle_d	24.137	729
X-RAY DIFFRACTION	f_chiral_restr	0.074	320
X-RAY DIFFRACTION	f_plane_restr	0.006	373

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.4994-1.532	0.2382	139	0.2169	2638	X-RAY DIFFRACTION	100
1.532-1.5677	0.2193	140	0.2017	2646	X-RAY DIFFRACTION	100
1.5677-1.6069	0.2103	141	0.1853	2694	X-RAY DIFFRACTION	100
1.6069-1.6503	0.1919	140	0.182	2645	X-RAY DIFFRACTION	100
1.6503-1.6989	0.1941	140	0.1651	2673	X-RAY DIFFRACTION	100
1.6989-1.7537	0.1862	142	0.1505	2695	X-RAY DIFFRACTION	100
1.7537-1.8164	0.188	140	0.1504	2655	X-RAY DIFFRACTION	100
1.8164-1.8892	0.1778	140	0.1472	2671	X-RAY DIFFRACTION	100
1.8892-1.9751	0.1864	142	0.144	2695	X-RAY DIFFRACTION	100
1.9751-2.0793	0.1613	142	0.1477	2684	X-RAY DIFFRACTION	100
2.0793-2.2095	0.1522	142	0.1416	2699	X-RAY DIFFRACTION	100
2.2095-2.3801	0.1618	142	0.142	2704	X-RAY DIFFRACTION	100
2.3801-2.6196	0.1604	142	0.1413	2705	X-RAY DIFFRACTION	100
2.6196-2.9986	0.1478	145	0.1516	2744	X-RAY DIFFRACTION	100
2.9986-3.7777	0.1693	145	0.1472	2749	X-RAY DIFFRACTION	100
3.7777-45.8073	0.1496	153	0.1461	2904	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	0.0997	-0.0496	-0.005	0.1341	-0.0048	0.1463	0.0152	0.003	0.1391	-0.0722	0.0101	0.0221	-0.0806	-0.0046	0	0.1522	-0.0005	-0.0042	0.1196	-0.0035	0.1347	-1.6659	-19.0991	-13.4968
2	0.0273	-0.0265	0.0254	0.025	-0.0243	0.0233	0.0548	0.0256	-0.1139	0.0235	-0.0801	0.1821	0.1036	-0.3029	-0.0001	0.191	0.0083	-0.0308	0.1721	-0.0089	0.1743	-9.1915	-21.8359	-24.9969
3	0.1566	-0.0275	0.052	0.1264	-0.038	0.0638	0.0025	0.0951	0.1978	-0.2542	0.1805	-0.2706	-0.0601	-0.048	0.0025	0.2023	-0.0071	-0.0065	0.144	-0.0095	0.152	-3.6323	-20.4731	-25.3194
4	0.1599	0.077	0.0296	0.2459	-0.1569	0.1334	-0.0222	0.0715	-0.0046	-0.1109	0.0356	0.0129	-0.0257	0.0037	0	0.1505	-0.0128	0.0009	0.1251	0.0027	0.1168	1.0867	-26.2346	-22.2655
5	0.0623	0.0073	-0.0442	0.075	-0.0153	0.032	0.0288	0.1769	0.0979	-0.2814	0.0798	0.3279	0.0525	-0.2014	0.0097	0.2244	-0.0212	-0.0786	0.1865	0.0284	0.1928	-10.8918	-49.743	-25.0318
6	0.1204	-0.0677	0.1478	0.4086	-0.0198	0.193	0.0002	0.0243	-0.0191	-0.0578	0.0176	-0.0104	-0.0024	0.0213	-0	0.1311	-0.0042	0.004	0.1209	-0.0045	0.1332	2.6925	-36.7521	-15.9553
7	0.0487	-0.0169	0.076	0.1996	0.1516	0.2788	-0.0227	-0.0632	0.1369	-0.0202	-0.0141	0.0126	-0.0298	-0.0582	-0	0.1213	0.0019	-0.0086	0.1141	0.0045	0.1386	-3.0857	-31.6515	-10.37
8	0.0378	0.1434	-0.0925	0.8874	-0.4642	0.2653	-0.066	0.0591	0.0104	-0.2457	0.0509	0.3961	0.312	-0.858	-0.0219	0.1659	-0.0752	-0.0326	0.4379	0.0066	0.2443	-24.4577	-36.3691	-12.3745
9	0.2254	0.0484	0.1593	0.0849	-0.136	0.4885	0.0302	-0.0239	-0.0758	0.0273	-0.0103	-0.0196	-0.0102	-0.077	0	0.1292	-0.0026	0.0002	0.1343	0.0045	0.1281	-5.5277	-31.3666	-2.392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:37)
2	X-RAY DIFFRACTION	2	(chain A and resid 38:49)
3	X-RAY DIFFRACTION	3	(chain A and resid 50:67)
4	X-RAY DIFFRACTION	4	(chain A and resid 68:97)
5	X-RAY DIFFRACTION	5	(chain A and resid 98:109)
6	X-RAY DIFFRACTION	6	(chain A and resid 110:174)
7	X-RAY DIFFRACTION	7	(chain A and resid 175:191)
8	X-RAY DIFFRACTION	8	(chain A and resid 192:211)
9	X-RAY DIFFRACTION	9	(chain A and resid 212:253)