FAIRMol

Z19129319

Pose ID 14891 Compound 5539 Pose 653

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 Z19129319

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
31.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.81, Jaccard 0.63, H-bond role recall 0.36
Burial
90%
Hydrophobic fit
82%
Reason: 1 severe internal clashes, 6 internal clashes
1 severe internal clashes 6 protein-contact clashes 6 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (13/20 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 GDS: SAFE UL GreenDrugScore ML model
ECOscore
0.902
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.663
ADMET + ECO + DL
ADMETscore (GDS)
0.706
absorption · distr. · metab.
DLscore
0.445
drug-likeness
P(SAFE)
0.83
GDS classification
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.407 kcal/mol/HA) ✓ Good fit quality (FQ -13.28) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (31.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-39.385
kcal/mol
LE
-1.407
kcal/mol/HA
Fit Quality
-13.28
FQ (Leeson)
HAC
28
heavy atoms
MW
399
Da
LogP
2.21
cLogP
Final rank
4.1104
rank score
Inter norm
-1.093
normalised
Contacts
23
H-bonds 6
Strain ΔE
31.1 kcal/mol
SASA buried
90%
Lipo contact
82% BSA apolar/total
SASA unbound
667 Ų
Apolar buried
488 Ų

Interaction summary

HBD 1 HBA 5 HY 2 PI 1 CLASH 6 Severe 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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 overlap17Native recall0.81
Jaccard0.63RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
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
653 4.110379282357317 -1.09347 -39.3854 6 23 17 0.81 0.36 - 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 -39.385kcal/mol
Ligand efficiency (LE) -1.4066kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.279
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 399.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.78kcal/mol
Minimised FF energy 59.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 667.0Ų
Total solvent-accessible surface area of free ligand
BSA total 598.4Ų
Buried surface area upon binding
BSA apolar 487.7Ų
Hydrophobic contacts buried
BSA polar 110.8Ų
Polar contacts buried
Fraction buried 89.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1420.0Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 497.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)