FAIRMol

GemmaOHDUnisi_40

Pose ID 14577 Compound 3276 Pose 339

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 GemmaOHDUnisi_40

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
11.5 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.62, Jaccard 0.45, H-bond role recall 0.27
Burial
85%
Hydrophobic fit
83%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 75% of hydrophobic surface is solvent-exposed (18/24 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: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.385
ADMET + ECO + DL
ADMETscore (GDS)
0.409
absorption · distr. · metab.
DLscore
0.403
drug-likeness
P(SAFE)
0.15
GDS classification
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.972 kcal/mol/HA) ✓ Good fit quality (FQ -9.28) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (11.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-28.192
kcal/mol
LE
-0.972
kcal/mol/HA
Fit Quality
-9.28
FQ (Leeson)
HAC
29
heavy atoms
MW
386
Da
LogP
5.42
cLogP
Final rank
4.4425
rank score
Inter norm
-1.035
normalised
Contacts
21
H-bonds 8
Strain ΔE
11.5 kcal/mol
SASA buried
85%
Lipo contact
83% BSA apolar/total
SASA unbound
672 Ų
Apolar buried
472 Ų

Interaction summary

HBD 1 HBA 5 HY 2 PI 1 CLASH 6

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 overlap13Native recall0.62
Jaccard0.45RMSD-
HB strict3Strict recall0.20
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

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
349 2.334954596224445 -0.891673 -21.5588 6 15 0 0.00 0.00 - no Open
349 2.3660185072734445 -0.82669 -23.4712 6 16 0 0.00 0.00 - no Open
339 4.442510039643324 -1.03505 -28.1925 8 21 13 0.62 0.27 - 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 -28.192kcal/mol
Ligand efficiency (LE) -0.9722kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.280
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.42
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 83.87kcal/mol
Minimised FF energy 72.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 672.0Ų
Total solvent-accessible surface area of free ligand
BSA total 569.2Ų
Buried surface area upon binding
BSA apolar 472.0Ų
Hydrophobic contacts buried
BSA polar 97.3Ų
Polar contacts buried
Fraction buried 84.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1396.1Ų
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 527.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)