8BLP | pdb_00008blp

Human Urea Transporter UT-B/UT1 in Complex with Inhibitor UTBinh-14

PDB DOI: https://doi.org/10.2210/pdb8BLP/pdb
EM Map EMD-16112: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2022-11-10 Released: 2023-10-04
Deposition Author(s): Chi, G., Dietz, L., Pike, A.C.W., Maclean, E.M., Mukhopadhyay, S.M.M., Bohstedt, T., Wang, D., Scacioc, A., McKinley, G., Arrowsmith, C.H., Edwards, A., Bountra, C., Fernandez-Cid, A., Burgess-Brown, N.A., Duerr, K.L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural characterization of human urea transporters UT-A and UT-B and their inhibition.

Chi, G., Dietz, L., Tang, H., Snee, M., Scacioc, A., Wang, D., Mckinley, G., Mukhopadhyay, S.M.M., Pike, A.C.W., Chalk, R., Burgess-Brown, N.A., Timmermans, J.P., van Putte, W., Robinson, C.V., Durr, K.L.

(2023) Sci Adv 9: eadg8229-eadg8229

PubMed: 37774028 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adg8229
Primary Citation Related Structures:
8BLO, 8BLP

PubMed Abstract:
In this study, we present the structures of human urea transporters UT-A and UT-B to characterize them at molecular level and to detail the mechanism of UT-B inhibition by its selective inhibitor, UTB _inh-14. High-resolution structures of both transporters establish the structural basis for the inhibitor's selectivity to UT-B, and the identification of multiple binding sites for the inhibitor will aid with the development of drug lead molecules targeting both transporters. Our study also discovers phospholipids associating with the urea transporters by combining structural observations, native MS, and lipidomics analysis. These insights improve our understanding of urea transporter function at a molecular level and provide a blueprint for a structure-guided design of therapeutics targeting these transporters.

Organizational Affiliation

Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.

Macromolecule Content

Total Structure Weight: 155.17 kDa
Atom Count: 9,378
Modeled Residue Count: 1,065
Deposited Residue Count: 1,101
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter 1	A, B, C	367	Homo sapiens	Mutation(s): 1 Gene Names: SLC14A1, HUT11, JK, RACH1, UT1, UTE Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13336 (Homo sapiens) Explore Q13336 Go to UniProtKB: Q13336
PHAROS: Q13336 GTEx: ENSG00000141469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13336
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain DB [auth C] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain XA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain XA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain XA [auth C]	BA [auth B] D [auth A] DB [auth C] HA [auth B] J [auth A] BA [auth B], D [auth A], DB [auth C], HA [auth B], J [auth A], XA [auth C]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain BA [auth B] Focus chain D [auth A] Focus chain DB [auth C] Focus chain HA [auth B] Focus chain J [auth A] Focus chain XA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain D [auth A] Focus chain DB [auth C] Focus chain HA [auth B] Focus chain J [auth A] Focus chain XA [auth C]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain H [auth A] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain L [auth A] SDF format, chain LB [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain WA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain LA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth B]	AA [auth B] AB [auth C] BB [auth C] CA [auth B] CB [auth C] AA [auth B], AB [auth C], BB [auth C], CA [auth B], CB [auth C], DA [auth B], E [auth A], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HB [auth C], I [auth A], IA [auth B], IB [auth C], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], U [auth A], WA [auth C], Y [auth A], YA [auth C], ZA [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain ZA [auth C]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain VA [auth C] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth B]	VA [auth C], X [auth A], Z [auth B]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain VA [auth C] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain VA [auth C] Focus chain X [auth A] Focus chain Z [auth B]
5D3 (Subject of Investigation/LOI) Query on 5D3 Download:Ideal Coordinates CCD File SDF format, chain PB [auth C] SDF format, chain QB [auth C] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	PB [auth C] QB [auth C] TA [auth B] UA [auth B] V [auth A] PB [auth C], QB [auth C], TA [auth B], UA [auth B], V [auth A], W [auth A]	10-(4-ethylphenyl)sulfonyl-~{N}-(thiophen-2-ylmethyl)-5-thia-1,8,11,12-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,7,9,11-pentaen-7-amine C₂₀ H₁₇ N₅ O₂ S₃ UYFZCWXRMHSLTC-UHFFFAOYSA-N		Interactions Focus chain PB [auth C] Focus chain QB [auth C] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain PB [auth C] Focus chain QB [auth C] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A]