FAIRMol

OHD_Leishmania_125

Pose ID 7458 Compound 2914 Pose 6

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
T12
T. brucei R5P T. brucei
Ligand OHD_Leishmania_125
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
68.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.76, H-bond role recall 0.60
Burial
70%
Hydrophobic fit
75%
Reason: strain 68.4 kcal/mol
strain ΔE 68.4 kcal/mol 1 protein-contact clashes 36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.579 kcal/mol/HA) ✓ Good fit quality (FQ -6.01) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (68.4 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (19)
Score
-22.570
kcal/mol
LE
-0.579
kcal/mol/HA
Fit Quality
-6.01
FQ (Leeson)
HAC
39
heavy atoms
MW
528
Da
LogP
2.24
cLogP
Final rank
2.8313
rank score
Inter norm
-0.695
normalised
Contacts
21
H-bonds 11
Strain ΔE
68.4 kcal/mol
SASA buried
70%
Lipo contact
75% BSA apolar/total
SASA unbound
751 Ų
Apolar buried
392 Ų

Interaction summary

HBD 2 HBA 5 HY 4 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap16Native recall1.00
Jaccard0.76RMSD-
HB strict7Strict recall0.58
HB same residue+role6HB role recall0.60
HB same residue6HB residue recall0.60

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
10 1.5486714802125272 -1.05532 -40.4499 7 19 0 0.00 0.00 - no Open
7 2.547869714882232 -0.969977 -38.7032 9 19 0 0.00 0.00 - no Open
6 2.8312568440066483 -0.69453 -22.5704 11 21 16 1.00 0.60 - 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 -22.570kcal/mol
Ligand efficiency (LE) -0.5787kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.006
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 527.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.24
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 68.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 7.29kcal/mol
Minimised FF energy -61.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 751.4Ų
Total solvent-accessible surface area of free ligand
BSA total 522.0Ų
Buried surface area upon binding
BSA apolar 391.5Ų
Hydrophobic contacts buried
BSA polar 130.5Ų
Polar contacts buried
Fraction buried 69.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2261.3Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 787.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)