7FV9 | pdb_00007fv9

PanDDA analysis group deposition -- PHIP in complex with Z1004253138

PDB DOI: https://doi.org/10.2210/pdb7FV9/pdb
Deposition Group: G_1002265 (changed state) ExploreG_1002265

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-09 Released: 2023-03-29
Deposition Author(s): Grosjean, H., Tomlinson, C., Bradshaw, W.J., Koekemoer, L., Krojer, T., Fearon, D., Biggin, P.C., von Delft, F.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free:
0.227 (Depositor), 0.270 (DCC)
R-Value Work:
0.185 (Depositor), 0.240 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure-activity relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures

Grosjean, H., Fieseler, K.K., Sanchez-Garcia, R., Thompson, W., Deane, C.M., von Delft, F., Biggin, P.C.

(2026) Chem Sci

DOI: https://doi.org/10.1039/D5SC04919A

Macromolecule Content

Total Structure Weight: 17.96 kDa
Atom Count: 1,258
Modeled Residue Count: 121
Deposited Residue Count: 149
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A	149	Homo sapiens	Mutation(s): 0 Gene Names: PHIP, DCAF14, WDR11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWQ0 (Homo sapiens) Explore Q8WWQ0 Go to UniProtKB: Q8WWQ0
PHAROS: Q8WWQ0 GTEx: ENSG00000146247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WWQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZLC (Subject of Investigation/LOI) Query on ZLC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(5-methylfuran-2-carbonyl)-N-[(thiophen-2-yl)methyl]piperazine-1-carboxamide C₁₆ H₁₉ N₃ O₃ S FSJIDIRPKORUPE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free: 0.227 (Depositor), 0.270 (DCC)
R-Value Work: 0.185 (Depositor), 0.240 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.711	α = 90
b = 27.47	β = 100.42
c = 56.685	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-03-29
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection
Version 1.2: 2026-01-21
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.