jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM2579. This Compound is an exact match to PDB HET ID STU in crystal structure 1NVR, and this crystal structure was used to guide the docking calculations.

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JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__66757714222474__ initializing

Jmol getValue debug null

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Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__66757714222474__)

vwrOptions:

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setting document base to "https://bindingdb.org/rwd/bind/surflex.jsp?HET=STU&PDB=1NVR"

Jmol Version: 14.4.3_2016.03.02 2016-03-02 09:52

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java.version: 2016-03-02 13:00:37 (JSmol/j2s)

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FileManager.getAtomSetCollectionFromFile(../../data/surflex/1NVR_STU/1NVR.pdb)

FileManager opening url https://bindingdb.org/data/surflex/1NVR_STU/1NVR.pdb

The Resolver thinks Pdb

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TRANSFERASE 04-FEB-03 XXXX

THE COMPLEX STRUCTURE OF CHECKPOINT KINASE

CHK1/STAUROSPORINE

Setting space group name to P 1 21 1

XXXX

Time for openFile(../../data/surflex/1NVR_STU/1NVR.pdb): 847 ms

reading 2420 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

2420 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

TRANSFERASE 04-FEB-03 XXXX

THE COMPLEX STRUCTURE OF CHECKPOINT KINASE

CHK1/STAUROSPORINE

XXXX

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FileManager.getAtomSetCollectionFromFile(../../data/surflex/1NVR_STU/1NVR_ligand1.mol2)

FileManager opening url https://bindingdb.org/data/surflex/1NVR_STU/1NVR_ligand1.mol2

The Resolver thinks Mol2

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1NVR_ligand1

Time for openFile(../../data/surflex/1NVR_STU/1NVR_ligand1.mol2): 1307 ms

reading 60 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

60 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

2 models

Compound	Structure File	Surflex Score*	Ki(nM)	IC50(nM)	Kd(nM)
Protein 1NVR
Reference STU, BDBM2579
BDBM2579	1NVR-results_2579.mol2	9.4222		1;0.16;0.19;0.14	3
BDBM6763	1NVR-results_6763.mol2	7.0755		15
BDBM17054	1NVR-results_17054.mol2	9.9561		10
BDBM17140	1NVR-results_17140.mol2	7.3562	15
BDBM50245342	1NVR-results_50245342.mol2	10.2348		3
BDBM50245343	1NVR-results_50245343.mol2	9.9621		30
BDBM50280450	1NVR-results_50280450.mol2	10.3504		10;6

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of STU from the 1NVR is used as reference for docking the others.
CSV file for this table; mol2 file for the ligands.
Docked with Surflex v2710. Full input and output files are here.
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