jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM31093. This Compound is an exact match to PDB HET ID ZZL in crystal structure 2X81, and this crystal structure was used to guide the docking calculations.

loadScript jmol-14.4.3_2016.03.02/j2s/core/package.js

loadScript jmol-14.4.3_2016.03.02/j2s/core/corejmol.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__7328501791665394__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__7328501791665394__)

vwrOptions:

{ "name":"jmolApplet0","allowJavaScript":true,"applet":true,"documentBase":"https://bindingdb.org/rwd/bind/surflex.jsp?HET=ZZL&PDB=2X81","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__7328501791665394__","codePath":"https://bindingdb.org/rwd/bind/jmol-14.4.3_2016.03.02/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"7328501791665394","bgcolor":"#FFFFFF" }

setting document base to "https://bindingdb.org/rwd/bind/surflex.jsp?HET=ZZL&PDB=2X81"

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

java.vendor: Java2Script (HTML5)

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

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

loadScript jmol-14.4.3_2016.03.02/j2s/core/corescript.z.js

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__7328501791665394__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(../../data/surflex/2X81_ZZL/2X81.pdb)

FileManager opening url https://bindingdb.org/data/surflex/2X81_ZZL/2X81.pdb

The Resolver thinks Pdb

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TRANSFERASE 05-MAR-10 XXXX

STRUCTURE OF AURORA A IN COMPLEX WITH MLN8054

Setting space group name to P 61 2 2

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Time for openFile(../../data/surflex/2X81_ZZL/2X81.pdb): 1295 ms

reading 1911 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

1911 atoms created

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

TRANSFERASE 05-MAR-10 XXXX

STRUCTURE OF AURORA A IN COMPLEX WITH MLN8054

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loadScript jmol-14.4.3_2016.03.02/j2s/core/corescriptmath.z.js

appendNew = true

FileManager.getAtomSetCollectionFromFile(../../data/surflex/2X81_ZZL/2X81_ligand0.mol2)

FileManager opening url https://bindingdb.org/data/surflex/2X81_ZZL/2X81_ligand0.mol2

The Resolver thinks Mol2

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loadScript jmol-14.4.3_2016.03.02/j2s/J/adapter/readers/more/ForceFieldReader.js

2X81_ligand0

Time for openFile(../../data/surflex/2X81_ZZL/2X81_ligand0.mol2): 1134 ms

reading 47 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

47 atoms created

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

2 models

Compound	Structure File	Surflex Score*	IC50(nM)	Kd(nM)
Protein 2X81
Reference ZZL, BDBM31093
BDBM31093	2X81-results_31093.mol2	8.3915	2;4	7
BDBM50277545	2X81-results_50277545.mol2	9.1908	4;0.69;0.60;1;7;100;0.04;13

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of ZZL from the 2X81 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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