FAIRMol

Z118508076

Pose ID 14725 Compound 3848 Pose 487

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 Z118508076

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 medium Native strong SASA done
Strain ΔE
31.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.45
Burial
93%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.376
ADMET + ECO + DL
ADMETscore (GDS)
0.375
absorption · distr. · metab.
DLscore
0.434
drug-likeness
P(SAFE)
0.29
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.670 kcal/mol/HA) ✓ Good fit quality (FQ -14.96) ✓ Good H-bonds (4 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (31.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-40.071
kcal/mol
LE
-1.670
kcal/mol/HA
Fit Quality
-14.96
FQ (Leeson)
HAC
24
heavy atoms
MW
355
Da
LogP
4.35
cLogP
Final rank
1.9204
rank score
Inter norm
-1.370
normalised
Contacts
19
H-bonds 6
Strain ΔE
31.8 kcal/mol
SASA buried
93%
Lipo contact
70% BSA apolar/total
SASA unbound
581 Ų
Apolar buried
377 Ų

Interaction summary

HBA 4 HY 2 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 overlap16Native recall0.76
Jaccard0.67RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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
467 0.19455200423800365 -1.29947 -28.6657 3 17 0 0.00 0.00 - no Open
470 1.5588883286034063 -1.12198 -36.4577 7 17 0 0.00 0.00 - no Open
487 1.9203568414870582 -1.37015 -40.0712 6 19 16 0.76 0.45 - 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 -40.071kcal/mol
Ligand efficiency (LE) -1.6696kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.963
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.35
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 17.84kcal/mol
Minimised FF energy -13.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 581.4Ų
Total solvent-accessible surface area of free ligand
BSA total 540.1Ų
Buried surface area upon binding
BSA apolar 377.2Ų
Hydrophobic contacts buried
BSA polar 162.8Ų
Polar contacts buried
Fraction buried 92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1277.5Ų
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 495.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)