7XN9

Crystal structure of SSTR2 and L-054,522 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into ligand recognition and selectivity of somatostatin receptors.

Zhao, W.Han, S.Qiu, N.Feng, W.Lu, M.Zhang, W.Wang, M.Zhou, Q.Chen, S.Xu, W.Du, J.Chu, X.Yi, C.Dai, A.Hu, L.Shen, M.Y.Sun, Y.Zhang, Q.Ma, Y.Zhong, W.Yang, D.Wang, M.W.Wu, B.Zhao, Q.

(2022) Cell Res 32: 761-772

  • DOI: https://doi.org/10.1038/s41422-022-00679-x
  • Primary Citation of Related Structures:  
    7XMR, 7XMS, 7XMT, 7XN9, 7XNA

  • PubMed Abstract: 

    Somatostatin receptors (SSTRs) play versatile roles in inhibiting the secretion of multiple hormones such as growth hormone and thyroid-stimulating hormone, and thus are considered as targets for treating multiple tumors. Despite great progress made in therapeutic development against this diverse receptor family, drugs that target SSTRs still show limited efficacy with preferential binding affinity and conspicuous side-effects. Here, we report five structures of SSTR2 and SSTR4 in different states, including two crystal structures of SSTR2 in complex with a selective peptide antagonist and a non-peptide agonist, respectively, a cryo-electron microscopy (cryo-EM) structure of G i1 -bound SSTR2 in the presence of the endogenous ligand SST-14, as well as two cryo-EM structures of G i1 -bound SSTR4 in complex with SST-14 and a small-molecule agonist J-2156, respectively. By comparison of the SSTR structures in different states, molecular mechanisms of agonism and antagonism were illustrated. Together with computational and functional analyses, the key determinants responsible for ligand recognition and selectivity of different SSTR subtypes and multiform binding modes of peptide and non-peptide ligands were identified. Insights gained in this study will help uncover ligand selectivity of various SSTRs and accelerate the development of new molecules with better efficacy by targeting SSTRs.


  • Organizational Affiliation

    State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Somatostatin receptor type 2,Endo-1,4-beta-xylanase589Homo sapiensNiallia circulansMutation(s): 0 
Gene Names: SSTR2xlnA
EC: 3.2.1.8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30874 (Homo sapiens)
Explore P30874 
Go to UniProtKB:  P30874
GTEx:  ENSG00000180616 
Find proteins for P09850 (Niallia circulans)
Explore P09850 
Go to UniProtKB:  P09850
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP30874P09850
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GI9 (Subject of Investigation/LOI)
Query on GI9

Download Ideal Coordinates CCD File 
C [auth A]tert-butyl (2S)-6-azanyl-2-[[(2R,3S)-3-(1H-indol-3-yl)-2-[[4-(2-oxidanylidene-3H-benzimidazol-1-yl)piperidin-1-yl]carbonylamino]butanoyl]amino]hexanoate
C35 H47 N7 O5
WFCIXKAZBUIFTR-PKIMSIDOSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
B [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.52α = 90
b = 97.957β = 90
c = 170.499γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32161133011
National Science Foundation (NSF, China)China31825010
National Science Foundation (NSF, China)China82121005
National Science Foundation (NSF, China)China81872915
National Science Foundation (NSF, China)China82073904
National Science Foundation (NSF, China)China81773792
National Science Foundation (NSF, China)China81973373
National Science Foundation (NSF, China)China21704064

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description