FAIRMol

OSA_Lib_1

Pose ID 14355 Compound 4523 Pose 117

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
T22
L. donovani rab5a L. donovani
Ligand OSA_Lib_1

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
20.4 kcal/mol
Protein clashes
0
Internal clashes
19
Native overlap
contact recall 0.57, Jaccard 0.44, H-bond role recall 0.09
Burial
80%
Hydrophobic fit
100%
Reason: 19 internal clashes
19 intramolecular clashes 85% of hydrophobic surface is solvent-exposed (28/33 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
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 (-0.725 kcal/mol/HA) ✓ Good fit quality (FQ -7.43) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (100%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-26.841
kcal/mol
LE
-0.725
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
37
heavy atoms
MW
535
Da
LogP
6.78
cLogP
Final rank
1.4196
rank score
Inter norm
-0.812
normalised
Contacts
18
H-bonds 1
Strain ΔE
20.4 kcal/mol
SASA buried
80%
Lipo contact
100% BSA apolar/total
SASA unbound
794 Ų
Apolar buried
632 Ų

Interaction summary

HBA 1 HY 2 PI 0 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap12Native recall0.57
Jaccard0.44RMSD-
HB strict1Strict recall0.07
HB same residue+role1HB role recall0.09
HB same residue1HB residue recall0.09

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
117 1.4195580406870996 -0.812234 -26.8411 1 18 12 0.57 0.09 - no Current
138 1.8344116519649407 -0.642811 -21.6456 1 16 0 0.00 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 -26.841kcal/mol
Ligand efficiency (LE) -0.7254kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.427
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 534.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 133.19kcal/mol
Minimised FF energy 112.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 793.7Ų
Total solvent-accessible surface area of free ligand
BSA total 632.9Ų
Buried surface area upon binding
BSA apolar 632.5Ų
Hydrophobic contacts buried
BSA polar 0.4Ų
Polar contacts buried
Fraction buried 79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 99.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1611.1Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 550.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)