8V1F

TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol

PDB DOI: https://doi.org/10.2210/pdb8V1F/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-11-20 Released: 2024-02-07
Deposition Author(s): Fraser, B.J., Dong, A., Kutera, M., Seitova, A., Li, Y., Hutchinson, A., Edwards, A., Benard, F., Halabelian, L., Arrowsmith, C., Structural Genomics Consortium (SGC)
Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.223
R-Value Work: 0.172
R-Value Observed: 0.172

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol

Fraser, B.J., Dong, A., Kutera, M., Seitova, A., Li, Y., Hutchinson, A., Edwards, A., Benard, F., Halabelian, L., Arrowsmith, C., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 84.38 kDa
Atom Count: 5,926
Modelled Residue Count: 693
Deposited Residue Count: 718
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2 non-catalytic chain	A, C	110	Homo sapiens	Mutation(s): 5 Gene Names: TMPRSS2, PRSS10
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393 Go to UniProtKB: O15393
PHAROS: O15393 GTEx: ENSG00000184012
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15393
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C	Go to GlyGen: O15393-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protease serine 2	B, D	249	Homo sapiens	Mutation(s): 0 Gene Names: TMPRSS2
UniProt & NIH Common Fund Data Resources
Find proteins for O15393 (Homo sapiens) Explore O15393 Go to UniProtKB: O15393
PHAROS: O15393 GTEx: ENSG00000184012
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15393
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D]	BA [auth C], JA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain Y [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain Y [auth C]	CA [auth C], Y [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth C] Focus chain Y [auth C]
7R8 (Subject of Investigation/LOI) Query on 7R8 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain O [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain O [auth B]	FA [auth D], O [auth B]	6-oxidanylnaphthalene-2-carboximidamide C₁₁ H₁₀ N₂ O ULKSSXOMKDEKPC-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain O [auth B] Interactions & Density Focus chain FA [auth D] Focus chain O [auth B]
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain P [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth B]	EA [auth D], G [auth A], N [auth B], P [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain P [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C]	X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth C] GA [auth D] HA [auth D] I [auth A] IA [auth D] AA [auth C], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], KA [auth D], L [auth B], LA [auth D], M [auth B], MA [auth D], NA [auth D], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Z [auth C]	DA [auth D], H [auth A], Z [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.223
R-Value Work: 0.172
R-Value Observed: 0.172
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.939	α = 90
b = 172.573	β = 90
c = 83.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN154328
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM124165