PDB-5o7c: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi...

Basic information

• Entry: Database: PDB / ID: 5o7c
• Title: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal quinoline based inhibitor
• Components: 17-beta-hydroxysteroid dehydrogenase 14
• Keywords: OXIDOREDUCTASE / non-steroidal inhibitor / 17beta-HSD14 / quinoline based inhibitors

Function / homology

Function:

Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 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-9N2 / beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
• Authors: Bertoletti, N. / Braun, F. / Heine, A. / 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	Jun 8, 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:

• 29.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	29,842	5
Polymers	28,683	1
Non-polymers	1,159	4
Water	3,927	218

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 spectrometry
• 119 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	119,366	20
Polymers	114,731	4
Non-polymers	4,635	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_455	-x-1,-y,z	1
crystal symmetry operation	5_455	-x-1,y,-z	1
crystal symmetry operation	6_555	x,-y,-z	1

Calculated values:

Buried area	21790 Å2
ΔGint	-199 kcal/mol
Surface area	32340 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	91.222, 91.222, 131.883
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-446- HOH
2	1	A-592- 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, 221 molecules

#2: Chemical

A-301 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Details:

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

#3: Chemical

A-302 ChemComp-NA / SODIUM ION

Details:

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

#5: Chemical

A-304 ChemComp-9N2 / 2-(4-fluoranyl-3-oxidanyl-phenyl)carbonylquinoline-7-carbonitrile

Details:

Mass: 292.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₉FN₂O₂

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.39 ų/Da / Density % sol: 48.65 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 6000 20%, HEPES 0.1 M pH 7.00, 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: 1.6→50 Å / Num. obs: 36906 / % possible obs: 99.5 % / Redundancy: 8.5 % / R_sym value: 0.075 / Net I/σ(I): 17.37
• Reflection shell: Resolution: 1.6→1.7 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.52 / Num. unique obs: 5872 / R_sym value: 0.475 / % possible all: 99.8

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: 1.6→46.111 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.67

	Rfactor	Num. reflection	% reflection
Rfree	0.1867	1846	5 %
Rwork	0.1597	-	-
obs	0.161	36900	99.52 %

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

Refinement step

Cycle: LAST / Resolution: 1.6→46.111 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1857	0	79	218	2154

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2006
X-RAY DIFFRACTION	f_angle_d	0.993	2748
X-RAY DIFFRACTION	f_dihedral_angle_d	15.419	1213
X-RAY DIFFRACTION	f_chiral_restr	0.06	322
X-RAY DIFFRACTION	f_plane_restr	0.007	400

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.5988-1.642	0.3121	139	0.2515	2640	X-RAY DIFFRACTION	100
1.642-1.6903	0.2751	141	0.2263	2670	X-RAY DIFFRACTION	100
1.6903-1.7449	0.2647	141	0.2057	2678	X-RAY DIFFRACTION	100
1.7449-1.8072	0.2465	139	0.1857	2645	X-RAY DIFFRACTION	100
1.8072-1.8796	0.2015	139	0.1804	2641	X-RAY DIFFRACTION	99
1.8796-1.9651	0.178	141	0.1717	2675	X-RAY DIFFRACTION	99
1.9651-2.0688	0.1997	140	0.17	2653	X-RAY DIFFRACTION	99
2.0688-2.1984	0.2242	141	0.159	2689	X-RAY DIFFRACTION	99
2.1984-2.3681	0.1721	141	0.1528	2685	X-RAY DIFFRACTION	99
2.3681-2.6064	0.1821	142	0.147	2696	X-RAY DIFFRACTION	100
2.6064-2.9835	0.1712	144	0.1498	2726	X-RAY DIFFRACTION	100
2.9835-3.7586	0.1732	145	0.1427	2752	X-RAY DIFFRACTION	100
3.7586-46.1301	0.15	153	0.1458	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	0.0523	0.0184	0.0377	0.068	-0.0154	0.1139	0.0358	0.0615	-0.0016	0.0396	-0.008	-0.0608	-0.0507	0.1109	-0	0.1096	-0.004	-0.0094	0.1503	0.0014	0.146	-19.0199	1.6983	-13.4583
2	0.0196	0.0117	-0.0098	0.0133	-0.0138	0.0147	0.016	0.0252	0.0941	-0.1208	0.0414	0.0546	-0.1772	-0.0987	-0.0001	0.1708	-0.0163	0.0093	0.2049	0.0075	0.1773	-21.616	9.1826	-25.1541
3	0.0348	0.0291	-0.0441	0.1546	-0.0122	0.0593	0.1518	0.2202	-0.1306	-0.0862	-0.021	-0.167	-0.0344	0.0017	0.0007	0.134	0.0058	-0.0076	0.2052	0.0191	0.1659	-20.299	3.7075	-25.2214
4	0.2358	-0.0189	-0.1517	0.1583	-0.0045	0.0976	0.0598	0.1265	0.039	-0.0571	-0.0534	-0.0059	0.0051	0.0128	0.0001	0.1397	0.0186	0.0035	0.163	0.0095	0.1321	-26.0994	-0.8955	-22.0425
5	0.0696	0.004	-0.0067	0.061	0.0376	0.0251	0.0464	0.1554	0.2523	-0.104	0.0302	-0.1808	-0.0459	-0.0395	-0.003	0.1752	0.0217	0.0301	0.2184	0.0695	0.1894	-49.5588	10.8826	-24.9524
6	0.371	0.0554	-0.123	0.0707	-0.1132	0.1829	0.0142	0.0494	0.0073	-0.0107	0.0053	-0.0039	0.0333	0.0016	-0	0.1162	0.0027	-0.0092	0.1279	-0.005	0.1319	-36.5478	-2.7696	-15.7071
7	0.1024	0.0444	0.0752	0.0579	-0.0411	0.1904	0.0063	0.0092	-0.0025	0.0043	-0.0443	-0.051	-0.0358	0.0751	-0.0001	0.1156	-0.0005	0.0018	0.1164	0.0053	0.1365	-31.577	3.0845	-10.338
8	0.1155	-0.2007	-0.222	0.347	0.3843	0.4262	-0.0048	0.0903	0.0851	-0.1146	-0.1132	-0.1051	-0.5421	-0.1249	-0.1278	0.4656	0.0553	-0.0032	0.1419	0.035	0.2252	-36.6055	24.4236	-12.1979
9	0.0357	-0.0028	-0.1465	0.1975	-0.0505	0.5695	-0.0103	-0.0234	-0.0145	0.0346	0.0132	0.0514	-0.0964	0.0298	0	0.1321	-0.0029	0.0017	0.1253	0.0007	0.1222	-31.5454	5.6965	-2.3108

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 212:254)