4ZP5 | pdb_00004zp5

MAP4K4 in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb4ZP5/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Simulium sp. iridescent virus
Mutation(s): No

Deposited: 2015-05-07 Released: 2016-10-05
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.264 (Depositor), 0.270 (DCC)
R-Value Work:
0.229 (Depositor), 0.240 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of MAP4K4 complex

Liu, S.

To be published.

Macromolecule Content

Total Structure Weight: 70.88 kDa
Atom Count: 4,886
Modeled Residue Count: 584
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 4	A, B	309	Homo sapiens	Mutation(s): 0 Gene Names: MAP4K4, HGK, KIAA0687, NIK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O95819 (Homo sapiens) Explore O95819 Go to UniProtKB: O95819
PHAROS: O95819 GTEx: ENSG00000071054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95819
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4QG Query on 4QG 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-(4-chlorophenyl)-1,3-oxazol-2-yl]benzamide C₁₆ H₁₁ Cl N₂ O₂ DXIZWXGKFCRUNM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4QG	BindingDB: 4ZP5	IC50: min: 94, max: 1.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.264 (Depositor), 0.270 (DCC)
R-Value Work: 0.229 (Depositor), 0.240 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.633	α = 90
b = 91.386	β = 90
c = 97.528	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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.