5M0S
Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors
- PDB DOI: https://doi.org/10.2210/pdb5M0S/pdb
- Classification: HYDROLASE
- Organism(s): Rattus norvegicus
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2016-10-05 Released: 2017-08-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.286 
- R-Value Work: 0.238 
- R-Value Observed: 0.240 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 827 | Rattus norvegicus | Mutation(s): 4  Gene Names: Enpp2, Atx, Npps2 EC: 3.1.4.39 | ||
UniProt | |||||
Find proteins for Q64610 (Rattus norvegicus) Explore Q64610  Go to UniProtKB:  Q64610 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q64610 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G37135JQ GlyCosmos:  G37135JQ GlyGen:  G37135JQ |
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
7CW Query on 7CW | R [auth A] | [3,5-bis(chloranyl)phenyl]methyl ~{N}-[2-[[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]ethyl]carbamate C34 H50 Cl2 N2 O5 RGSSNYYHNQIMAB-ZSCMZCBDSA-N | |||
IOD Query on IOD | F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
GOL Query on GOL | EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | D [auth A], E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
SCN Query on SCN | AA [auth A] BA [auth A] CA [auth A] DA [auth A] T [auth A] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
NA Query on NA | S [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.286 
- R-Value Work: 0.238 
- R-Value Observed: 0.240 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 62.826 | α = 90 |
b = 88.857 | β = 103.08 |
c = 77.293 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-08-16  Deposition Author(s): Keune, W.-J., Heidebrecht, T., Perrakis, A.
Revision History (Full details and data files)
- Version 1.0: 2017-08-16
Type: Initial release - Version 1.1: 2019-10-16
Changes: Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary