3Q0Z | pdb_00003q0z

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5h-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid

PDB DOI: https://doi.org/10.2210/pdb3Q0Z/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Hepatitis C virus subtype 1b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-16 Released: 2011-04-27
Deposition Author(s): Sheriff, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.200 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Syntheses and initial evaluation of a series of indolo-fused heterocyclic inhibitors of the polymerase enzyme (NS5B) of the hepatitis C virus.

Zheng, X., Hudyma, T.W., Martin, S.W., Bergstrom, C., Ding, M., He, F., Romine, J., Poss, M.A., Kadow, J.F., Chang, C.H., Wan, J., Witmer, M.R., Morin, P., Camac, D.M., Sheriff, S., Beno, B.R., Rigat, K.L., Wang, Y.K., Fridell, R., Lemm, J., Qiu, D., Liu, M., Voss, S., Pelosi, L., Roberts, S.B., Gao, M., Knipe, J., Gentles, R.G.

(2011) Bioorg Med Chem Lett 21: 2925-2929

PubMed: 21486696 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.03.067
Primary Citation Related Structures:
3Q0Z

PubMed Abstract:
Herein, we present initial SAR studies on a series of bridged 2-arylindole-based NS5B inhibitors. The introduction of bridging elements between the indole N1 and the ortho-position of the 2-aryl moiety resulted in conformationally constrained heterocycles that possess multiple additional vectors for further exploration. The binding mode and pharmacokinetic (PK) properties of select examples, including: 13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[2,1-d][1,4]benzodiazepine-10-carboxylic acid (7) (IC(50)=0.07 μM, %F=18), are reported.

Organizational Affiliation

Discovery Chemistry and Candidate Optimization, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA. xiaofan.zheng@bms.com

Macromolecule Content

Total Structure Weight: 130.15 kDa
Atom Count: 9,133
Modeled Residue Count: 1,096
Deposited Residue Count: 1,148
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	574	Hepatitis C virus subtype 1b	Mutation(s): 0 Gene Names: NS5B EC: 2.7.7.48
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1)) Explore Q9WMX2 Go to UniProtKB: Q9WMX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WMX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
23E Query on 23E Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid C₃₈ H₃₈ N₄ O₅ HDBNVTWMHMMKNY-XMHGGMMESA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
SO4 Query on SO4 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] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain H [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] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [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] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.200 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.3	α = 90
b = 91.4	β = 90
c = 231.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Sheriff, S.

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description