jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM7960. This Compound is an exact match to PDB HET ID AX7 in crystal structure 3GN1, 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__5495814099897935__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__5495814099897935__)

vwrOptions:

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setting document base to "https://bindingdb.org/rwd/bind/surflex.jsp?HET=AX7&PDB=3GN1"

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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Jmol getValue APPLETREADYCallback Jmol._readyCallback

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Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

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FileManager.getAtomSetCollectionFromFile(../../data/surflex/3GN1_AX7/3GN1.pdb)

FileManager opening url https://bindingdb.org/data/surflex/3GN1_AX7/3GN1.pdb

The Resolver thinks Pdb

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OXIDOREDUCTASE 16-MAR-09 XXXX

STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRU

TERNARY COMPLEX WITH COFACTOR (NADP+) AND INHIBITOR (DDD00067

Setting space group name to P 1 21 1

XXXX

Time for openFile(../../data/surflex/3GN1_AX7/3GN1.pdb): 908 ms

reading 8634 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

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

model 1.1 alternative locations: AB

Default Van der Waals type for model set to Jmol

8634 atoms created

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

OXIDOREDUCTASE 16-MAR-09 XXXX

STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRU

TERNARY COMPLEX WITH COFACTOR (NADP+) AND INHIBITOR (DDD00067

XXXX

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FileManager.getAtomSetCollectionFromFile(../../data/surflex/3GN1_AX7/3GN1_ligand5.mol2)

FileManager opening url https://bindingdb.org/data/surflex/3GN1_AX7/3GN1_ligand5.mol2

The Resolver thinks Mol2

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

3GN1_ligand5

Time for openFile(../../data/surflex/3GN1_AX7/3GN1_ligand5.mol2): 1136 ms

reading 17 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

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

model 1.1 alternative locations: AB

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

17 atoms created

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

2 models

Compound	Structure File	Surflex Score*	Ki(nM)
Protein 3GN1
Reference AX7, BDBM7960
BDBM7960	3GN1-results_7960.mol2	2.9458	288000
BDBM31794	3GN1-results_31794.mol2	3.3360	10600
BDBM31796	3GN1-results_31796.mol2	0.3806	>200000

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of AX7 from the 3GN1 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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