FAIRMol

Z46032342

Pose ID 12044 Compound 4865 Pose 523

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 Z46032342
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 and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
6.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.37
Burial
69%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.3 kcal/mol) ✓ Excellent LE (-0.872 kcal/mol/HA) ✓ Good fit quality (FQ -7.43) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-18.305
kcal/mol
LE
-0.872
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
21
heavy atoms
MW
282
Da
LogP
3.06
cLogP
Strain ΔE
6.3 kcal/mol
SASA buried
69%
Lipo contact
83% BSA apolar/total
SASA unbound
520 Ų
Apolar buried
299 Ų

Interaction summary

HB 2 HY 20 PI 2 CLASH 1

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
Final rank1.646Score-18.305
Inter norm-0.981Intra norm0.110
Top1000noExcludedno
Contacts13H-bonds2
Artifact reasongeometry warning; 9 clashes; 1 protein clash
Residues
CYS52 GLU18 GLY13 GLY49 GLY50 ILE339 LEU17 MET113 SER14 THR335 TRP21 TYR110 VAL53

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 overlap7Native recall0.54
Jaccard0.37RMSD-
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
506 0.670504032085632 -1.17036 -22.7955 8 14 0 0.00 - - no Open
523 1.6456145987113313 -0.981172 -18.3048 2 13 7 0.54 - - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -18.305kcal/mol
Ligand efficiency (LE) -0.8717kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.435
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 282.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.06
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 6.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 83.33kcal/mol
Minimised FF energy 77.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 520.3Ų
Total solvent-accessible surface area of free ligand
BSA total 359.6Ų
Buried surface area upon binding
BSA apolar 299.0Ų
Hydrophobic contacts buried
BSA polar 60.6Ų
Polar contacts buried
Fraction buried 69.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3056.4Ų
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 1452.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)