9BBP | pdb_00009bbp

SARS-CoV-2 Mpro in complex with compound 12d inhibitor

PDB DOI: https://doi.org/10.2210/pdb9BBP/pdb

Classification: VIRAL PROTEIN, Hydrolase
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-04-07 Released: 2025-04-16
Deposition Author(s): Afsar, M., Bury, P., Olsen, S.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SARS-CoV-2 Mpro in complex with compound 12d inhibitor

Afsar, M., Bury, P., Olsen, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 34.77 kDa
Atom Count: 2,528
Modeled Residue Count: 301
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ALW (Subject of Investigation/LOI) Query on A1ALW Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	N-{(2R)-1-amino-3-[(2R,3S)-2-hydroxypyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-fluoropyridin-3-yl)benzoyl]-L-leucinamide C₂₅ H₃₄ F N₅ O₃ AGFPLVUVLJRIIL-DEXHYYOUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PHE (Subject of Investigation/LOI) Query on PHE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
THR (Subject of Investigation/LOI) Query on THR 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]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
VAL (Subject of Investigation/LOI) Query on VAL 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]	VALINE C₅ H₁₁ N O₂ KZSNJWFQEVHDMF-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLY (Subject of Investigation/LOI) Query on GLY 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]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.642	α = 90
b = 64.19	β = 90
c = 104.816	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Afsar, M.

Bury, P.

Olsen, S.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115568
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM128731
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR200030