6PDI | pdb_00006pdi

Human PIM1 bound to benzothiophene inhibitor 224

PDB DOI: https://doi.org/10.2210/pdb6PDI/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., Fala, A.M., Santiago, A.S., 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: 1.85 Å
R-Value Free:
0.193 (Depositor), 0.197 (DCC)
R-Value Work:
0.161 (Depositor), 0.171 (DCC)
R-Value Observed:
0.163 (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: 38.08 kDa
Atom Count: 2,497
Modeled Residue Count: 284
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCJ (Subject of Investigation/LOI) Query on OCJ 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-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide C₂₁ H₁₇ N₃ O₂ S₂ SDZHQRUPXPKDOD-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] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]