FAIRMol

OHD_Leishmania_287

Pose ID 8138 Compound 4034 Pose 8

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand OHD_Leishmania_287
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.57
Burial
77%
Hydrophobic fit
75%
Reason: 10 internal clashes
10 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.106 kcal/mol/HA) ✓ Good fit quality (FQ -9.76) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (15.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-25.441
kcal/mol
LE
-1.106
kcal/mol/HA
Fit Quality
-9.76
FQ (Leeson)
HAC
23
heavy atoms
MW
305
Da
LogP
3.74
cLogP
Final rank
3.8461
rank score
Inter norm
-1.309
normalised
Contacts
17
H-bonds 8
Strain ΔE
15.8 kcal/mol
SASA buried
77%
Lipo contact
75% BSA apolar/total
SASA unbound
565 Ų
Apolar buried
326 Ų

Interaction summary

HBD 1 HBA 6 HY 1 PI 3 CLASH 0

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
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap14Native recall0.74
Jaccard0.64RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue5HB residue recall0.71

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
8 3.846111606999529 -1.30865 -25.4412 8 17 14 0.74 0.57 - 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 -25.441kcal/mol
Ligand efficiency (LE) -1.1061kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.763
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 305.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.74
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 87.44kcal/mol
Minimised FF energy 71.65kcal/mol

SASA & burial

✓ computed
SASA (unbound) 565.4Ų
Total solvent-accessible surface area of free ligand
BSA total 434.3Ų
Buried surface area upon binding
BSA apolar 326.4Ų
Hydrophobic contacts buried
BSA polar 107.9Ų
Polar contacts buried
Fraction buried 76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2503.0Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1410.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)