Download MendeleyInvestigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures
Olajuyigbe, F.M., Demitri, N., Geremia, S.(2011) Cryst Growth Des 11: 4378-4385
3NDT
HIV-1 Protease Saquinavir:Ritonavir 1:1 complex structure
- PDB DOI: https://doi.org/10.2210/pdb3NDT/pdb
- Classification: hydrolase/hydrolase inhibitor
- Organism(s): Human immunodeficiency virus type 1 BH10
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2010-06-08 Released: 2011-07-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.229
- R-Value Work: 0.110
- R-Value Observed: 0.140
This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protease | 100 | Human immunodeficiency virus type 1 BH10 | Mutation(s): 5 Gene Names: gag-pol EC: 3.4.23.16 |  | |
UniProt | |||||
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P03366 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ROC Query on ROC | E [auth A], S [auth D] | (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1
-phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N |  | ||
| DMS Query on DMS | G [auth A], H [auth A], Q [auth C], R [auth C] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A] J [auth B] K [auth B] L [auth B] M [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | I [auth B], O [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Binding Affinity Annotations | |||
|---|---|---|---|
| ID | Source | Binding Affinity | |
| ROC | BindingDB: 3NDT | Ki: min: 0.04, max: 138 (nM) from 29 assay(s) | |
| Kd: min: 0.31, max: 67 (nM) from 6 assay(s) | |||
| IC50: min: 0.2, max: 270 (nM) from 16 assay(s) | |||
| -TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 47 assay(s) | |||
| ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 47 assay(s) | |||
| ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s) | |||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000454 (ROC) Query on PRD_000454 | E [auth A], S [auth D] | Saquinavir | Peptide-like / Inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.229
- R-Value Work: 0.110
- R-Value Observed: 0.140
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.294 | α = 90 |
| b = 62.785 | β = 98.32 |
| c = 59.171 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| SHELX | model building |
| SHELXL-97 | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHELX | phasing |
Entry History
Deposition Data
- Released Date: 2011-07-20 Deposition Author(s): Geremia, S., Olajuyigbe, F.M., Demitri, N.
Revision History (Full details and data files)
- Version 1.0: 2011-07-20
Type: Initial release - Version 1.1: 2011-12-07
Changes: Database references - Version 1.2: 2012-12-12
Changes: Other - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
