FAIRMol

OHD_TB2023_3

Pose ID 11584 Compound 3629 Pose 63

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 OHD_TB2023_3
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
21.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.56
Burial
53%
Hydrophobic fit
91%
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
vB — Very bioaccumulative (BCF>5000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.722 kcal/mol/HA) ✓ Good fit quality (FQ -7.39) ✓ Strong H-bond network (6 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ High strain energy (21.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-26.715
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-7.39
FQ (Leeson)
HAC
37
heavy atoms
MW
529
Da
LogP
6.90
cLogP
Final rank
4.2303
rank score
Inter norm
-0.612
normalised
Contacts
12
H-bonds 7
Strain ΔE
21.0 kcal/mol
SASA buried
53%
Lipo contact
91% BSA apolar/total
SASA unbound
828 Ų
Apolar buried
400 Ų

Interaction summary

HBD 5 HBA 1 HY 3 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap9Native recall0.69
Jaccard0.56RMSD-
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
61 1.3170867062113978 -0.700787 -22.9187 4 17 0 0.00 - - no Open
63 3.152214993807659 -0.692608 -25.8286 5 18 0 0.00 - - no Open
63 4.230266712277451 -0.612234 -26.7147 7 12 9 0.69 - - 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 -26.715kcal/mol
Ligand efficiency (LE) -0.7220kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.392
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 529.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.90
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -31.14kcal/mol
Minimised FF energy -52.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 827.7Ų
Total solvent-accessible surface area of free ligand
BSA total 439.7Ų
Buried surface area upon binding
BSA apolar 400.1Ų
Hydrophobic contacts buried
BSA polar 39.6Ų
Polar contacts buried
Fraction buried 53.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3247.7Ų
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 1587.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)