FAIRMol

Z28978240

Pose ID 12032 Compound 3657 Pose 511

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z28978240
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
13.9 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.62, Jaccard 0.38
Burial
69%
Hydrophobic fit
70%
Reason: 7 internal clashes
7 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.717 kcal/mol/HA) ✓ Good fit quality (FQ -6.92) ✓ Good H-bonds (4 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (13.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.516
kcal/mol
LE
-0.717
kcal/mol/HA
Fit Quality
-6.92
FQ (Leeson)
HAC
30
heavy atoms
MW
444
Da
LogP
2.50
cLogP
Strain ΔE
13.9 kcal/mol
SASA buried
69%
Lipo contact
70% BSA apolar/total
SASA unbound
701 Ų
Apolar buried
340 Ų

Interaction summary

HB 4 HY 23 PI 3 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank0.394Score-21.516
Inter norm-0.715Intra norm-0.002
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 7 clashes; 1 protein contact clash
Residues
CYS52 CYS57 FAD501 GLU18 GLY13 GLY49 ILE339 LEU17 MET113 PRO336 SER14 THR335 TRP21 TYR110 VAL53 VAL58

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap8Native recall0.62
Jaccard0.38RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
511 0.39436596976904614 -0.715154 -21.5162 4 16 8 0.62 - - no Current
483 1.7620362114443309 -0.816397 -22.9647 4 16 0 0.00 - - no Open
490 2.610889302737764 -0.661563 -19.5593 5 13 0 0.00 - - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -21.516kcal/mol
Ligand efficiency (LE) -0.7172kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.918
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 443.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.50
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -63.28kcal/mol
Minimised FF energy -77.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 701.2Ų
Total solvent-accessible surface area of free ligand
BSA total 486.2Ų
Buried surface area upon binding
BSA apolar 340.1Ų
Hydrophobic contacts buried
BSA polar 146.1Ų
Polar contacts buried
Fraction buried 69.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3131.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1483.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)