8X7H | pdb_00008x7h

Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).

PDB DOI: https://doi.org/10.2210/pdb8X7H/pdb

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

Deposited: 2023-11-24 Released: 2025-03-26
Deposition Author(s): Dong, C., Yan, X., Li, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.301 (Depositor), 0.301 (DCC)
R-Value Work:
0.235 (Depositor), 0.244 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 162

Dong, C., Yan, X., Li, Y.

To be published.

Macromolecule Content

Total Structure Weight: 142.61 kDa
Atom Count: 8,411
Modelled Residue Count: 1,070
Deposited Residue Count: 1,172
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-induced degradation protein 4 homolog	A, C, E, G	167	Homo sapiens	Mutation(s): 0 Gene Names: GID4, C17orf39, VID24
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVV7 (Homo sapiens) Explore Q8IVV7 Go to UniProtKB: Q8IVV7
PHAROS: Q8IVV7 GTEx: ENSG00000141034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IVV7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	B, D, F, H	126	Homo sapiens	Mutation(s): 0 Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885 Go to UniProtKB: O60885
PHAROS: O60885 GTEx: ENSG00000141867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YBI (Subject of Investigation/LOI) Query on YBI Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth G]	I [auth A], K [auth C], P [auth E], Q [auth G]	~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide C₅₀ H₅₆ Cl N₁₁ O₃ S WIURLZYDRMMHFO-BPKRYYIFSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain P [auth E] Focus chain Q [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain P [auth E] Focus chain Q [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth H] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H]	J [auth B] L [auth D] M [auth D] N [auth D] O [auth D] J [auth B], L [auth D], M [auth D], N [auth D], O [auth D], R [auth G], S [auth G], T [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain J [auth B] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.301 (Depositor), 0.301 (DCC)
R-Value Work: 0.235 (Depositor), 0.244 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.855	α = 103.09
b = 87.613	β = 90.9
c = 88.44	γ = 106.23

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Dong, C.

Yan, X.

Li, Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31900865
National Natural Science Foundation of China (NSFC)	China	32271265
National Natural Science Foundation of China (NSFC)	China	32071193

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

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Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 8X7H | pdb_00008x7h

Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).

Crystal structure of 162

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2