6PDN | pdb_00006pdn

Human PIM1 bound to benzothiophene inhibitor 292

PDB DOI: https://doi.org/10.2210/pdb6PDN/pdb

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

Deposited: 2019-06-19 Released: 2019-07-24
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: 2.40 Å
R-Value Free:
0.223 (Depositor), 0.233 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human PIM1

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: 37.72 kDa
Atom Count: 2,391
Modeled Residue Count: 278
Deposited Residue Count: 327
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	313	Homo sapiens	Mutation(s): 0 Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309 Go to UniProtKB: P11309
PHAROS: P11309 GTEx: ENSG00000137193
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	B	14	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OD4 (Subject of Investigation/LOI) Query on OD4 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-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxylic acid C₁₇ H₁₆ N₂ O₃ S₂ PPVOHCUEWCXUEU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.223 (Depositor), 0.233 (DCC)
R-Value Work: 0.188 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.001	α = 90
b = 98.001	β = 90
c = 80.248	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-24

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: 2019-07-24
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary