PDB-5o6x: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi...

Basic information

• Entry: Database: PDB / ID: 5o6x
• 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 / 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-9MK / beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 7, 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)	29,831	5
Polymers	28,683	1
Non-polymers	1,148	4
Water	4,432	246

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)	119,322	20
Polymers	114,731	4
Non-polymers	4,591	16
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	5_555	-x,y,-z	1
crystal symmetry operation	6_565	x,-y+1,-z	1

Calculated values:

Buried area	19800 Å2
ΔGint	-187 kcal/mol
Surface area	32720 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	91.132, 91.132, 133.345
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-517- HOH
2	1	A-645- 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 (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, 249 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-9MK / (4-fluoranyl-3-oxidanyl-phenyl)-(6-methylquinolin-2-yl)methanone

Details:

Mass: 281.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₂FNO₂

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.42 ų/Da / Density % sol: 49.11 %
• 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: 1.35→50 Å / Num. obs: 117838 / % possible obs: 99.9 % / Redundancy: 6.8 % / R_sym value: 0.059 / Net I/σ(I): 19.06
• Reflection shell: Resolution: 1.35→1.43 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.68 / Num. unique obs: 19085 / R_sym value: 0.519 / % possible all: 99.9

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: 1.35→46.335 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.77

	Rfactor	Num. reflection	% reflection
Rfree	0.1384	5885	4.99 %
Rwork	0.1181	-	-
obs	0.1191	117832	99.92 %

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

Refinement step

Cycle: LAST / Resolution: 1.35→46.335 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1840	0	78	246	2164

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2013
X-RAY DIFFRACTION	f_angle_d	0.947	2762
X-RAY DIFFRACTION	f_dihedral_angle_d	23.606	760
X-RAY DIFFRACTION	f_chiral_restr	0.074	324
X-RAY DIFFRACTION	f_plane_restr	0.006	402

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.3501-1.3654	0.1777	199	0.1718	3742	X-RAY DIFFRACTION	100
1.3654-1.3815	0.2023	199	0.1574	3793	X-RAY DIFFRACTION	100
1.3815-1.3983	0.18	195	0.1531	3656	X-RAY DIFFRACTION	100
1.3983-1.416	0.174	194	0.1472	3757	X-RAY DIFFRACTION	100
1.416-1.4346	0.1751	198	0.15	3681	X-RAY DIFFRACTION	99
1.4346-1.4543	0.1589	195	0.1334	3754	X-RAY DIFFRACTION	100
1.4543-1.4751	0.1298	195	0.119	3740	X-RAY DIFFRACTION	100
1.4751-1.4971	0.1404	200	0.114	3763	X-RAY DIFFRACTION	100
1.4971-1.5205	0.1347	194	0.1057	3731	X-RAY DIFFRACTION	100
1.5205-1.5454	0.1305	197	0.1011	3733	X-RAY DIFFRACTION	100
1.5454-1.5721	0.1154	196	0.0989	3754	X-RAY DIFFRACTION	100
1.5721-1.6007	0.1314	192	0.0963	3715	X-RAY DIFFRACTION	100
1.6007-1.6314	0.1319	190	0.1007	3714	X-RAY DIFFRACTION	100
1.6314-1.6647	0.1464	195	0.0998	3727	X-RAY DIFFRACTION	100
1.6647-1.7009	0.125	197	0.0978	3683	X-RAY DIFFRACTION	99
1.7009-1.7405	0.1213	198	0.0957	3750	X-RAY DIFFRACTION	100
1.7405-1.784	0.1069	196	0.0975	3767	X-RAY DIFFRACTION	100
1.784-1.8323	0.1248	194	0.0961	3689	X-RAY DIFFRACTION	100
1.8323-1.8862	0.1447	197	0.1004	3743	X-RAY DIFFRACTION	100
1.8862-1.9471	0.1172	200	0.1038	3742	X-RAY DIFFRACTION	100
1.9471-2.0167	0.1262	200	0.1064	3749	X-RAY DIFFRACTION	100
2.0167-2.0974	0.1321	189	0.1075	3709	X-RAY DIFFRACTION	100
2.0974-2.1929	0.1206	200	0.1037	3716	X-RAY DIFFRACTION	100
2.1929-2.3085	0.1265	194	0.1076	3731	X-RAY DIFFRACTION	100
2.3085-2.4531	0.1351	201	0.1087	3736	X-RAY DIFFRACTION	100
2.4531-2.6425	0.1427	201	0.1139	3730	X-RAY DIFFRACTION	100
2.6425-2.9084	0.1232	189	0.1216	3729	X-RAY DIFFRACTION	100
2.9084-3.3291	0.1513	197	0.1341	3727	X-RAY DIFFRACTION	100
3.3291-4.1939	0.1469	198	0.1286	3741	X-RAY DIFFRACTION	100
4.1939-46.3624	0.1546	195	0.1445	3745	X-RAY DIFFRACTION	100