6PK6

Human PRPF4B bound to benzothiophene inhibitor 329

PDB DOI: https://doi.org/10.2210/pdb6PK6/pdb

Classification: TRANSFERASE/TRANSFERASE Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-28 Released: 2019-08-28
Deposition Author(s): Godoi, P.H.C., Santiago, A.S., Fala, A.M., Ramos, P.Z., Sriranganadane, D., Mascarello, A., Segretti, N., Azevedo, H., Guimaraes, C.R.W., Arruda, P., Elkins, J.M., Counago, R.M., Structural Genomics Consortium (SGC)
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.216 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

to be published

Godoi, P.H.C., Santiago, A.S., Fala, A.M., Ramos, P.Z., Sriranganadane, D., Mascarello, A., Segretti, N., Azevedo, H., Guimaraes, C.R.W., Arruda, P., Elkins, J.M., Counago, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 41.45 kDa
Atom Count: 2,881
Modelled Residue Count: 338
Deposited Residue Count: 351
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PRP4 homolog	A	351	Homo sapiens	Mutation(s): 0 Gene Names: PRPF4B, KIAA0536, PRP4, PRP4H, PRP4K EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13523 (Homo sapiens) Explore Q13523 Go to UniProtKB: Q13523
PHAROS: Q13523 GTEx: ENSG00000112739
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13523
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OND (Subject of Investigation/LOI) Query on OND Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(5-{[(2-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide C₂₁ H₁₇ N₃ O₂ S₂ UQZFCZAYARDQIK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
OND	BindingDB: 6PK6	Ki: 1300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.132	α = 90
b = 69.132	β = 90
c = 104.533	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-06
Changes: Structure summary