FAIRMol

Z19652710

Pose ID 12038 Compound 1854 Pose 517

DB fairmolDocking 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 Z19652710
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 medium Native mixed SASA done
Strain ΔE
7.8 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.54, Jaccard 0.41
Burial
66%
Hydrophobic fit
59%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.8 kcal/mol) ✓ Excellent LE (-0.978 kcal/mol/HA) ✓ Good fit quality (FQ -8.18) ✓ Good H-bonds (4 bonds) ✓ Deep burial (66% SASA buried) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (5)
Score
-19.552
kcal/mol
LE
-0.978
kcal/mol/HA
Fit Quality
-8.18
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
3.32
cLogP
Strain ΔE
7.8 kcal/mol
SASA buried
66%
Lipo contact
59% BSA apolar/total
SASA unbound
530 Ų
Apolar buried
206 Ų

Interaction summary

HB 4 HY 15 PI 1 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 rank0.300Score-19.552
Inter norm-1.036Intra norm0.058
Top1000noExcludedno
Contacts11H-bonds4
Artifact reasongeometry warning; 5 clashes; 4 protein contact clashes
Residues
CYS52 GLU18 GLY13 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
Jaccard0.41RMSD-
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
488 0.07748725599830515 -1.09846 -21.111 5 11 0 0.00 - - no Open
517 0.29968302526280177 -1.03568 -19.5522 4 11 7 0.54 - - no Current
485 1.8038394012921375 -1.30437 -26.1579 3 11 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 -19.552kcal/mol
Ligand efficiency (LE) -0.9776kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.181
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 305.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.32
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -14.34kcal/mol
Minimised FF energy -22.15kcal/mol

SASA & burial

✓ computed
SASA (unbound) 530.2Ų
Total solvent-accessible surface area of free ligand
BSA total 350.9Ų
Buried surface area upon binding
BSA apolar 206.1Ų
Hydrophobic contacts buried
BSA polar 144.8Ų
Polar contacts buried
Fraction buried 66.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2966.1Ų
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 1470.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)