9Z5Z | pdb_00009z5z

Co-crystal structure of compound 3S bound to the Catalytic domain of human PAH

PDB DOI: https://doi.org/10.2210/pdb9Z5Z/pdb

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

Deposited: 2025-11-13 Released: 2026-10-21
Deposition Author(s): Hammoudeh, D., Padyana, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z5Z

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

Literature

Discovery of a pharmacological chaperone that stabilizes mutant forms of phenylalanine hydroxylase and significantly lowers blood phenylalanine in a classical phenylketonuria mouse model

Hammoudeh, D., Padyana, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.86 kDa
Atom Count: 2,846
Modeled Residue Count: 309
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine-4-hydroxylase	A	316	Homo sapiens	Mutation(s): 0 Gene Names: PAH EC: 1.14.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00439 (Homo sapiens) Explore P00439 Go to UniProtKB: P00439
PHAROS: P00439 GTEx: ENSG00000171759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00439
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C05( Subject of Investigation/LOI) Query on A1C05 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]	1-[(4S)-4-(1-benzofuran-2-yl)-1,4,6,7-tetrahydro-5H-imidazo[4,5-c]pyridin-5-yl]-3-(1,3-thiazol-2-yl)propan-1-one C₂₀ H₁₈ N₄ O₂ S NINHBCVEDCFQPV-HXUWFJFHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.84	α = 90
b = 107.48	β = 90
c = 123.8	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-10-21
Type: Initial release