FAIRMol

Z32301499

Pose ID 14675 Compound 4079 Pose 437

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
T22
L. donovani rab5a L. donovani
Ligand Z32301499

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
32.8 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.81, Jaccard 0.63, H-bond role recall 0.36
Burial
81%
Hydrophobic fit
83%
Reason: 8 internal clashes
8 protein-contact clashes 8 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (12/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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.
Not B (BCF≤2000)
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 (-0.905 kcal/mol/HA) ✓ Good fit quality (FQ -8.98) ✓ Good H-bonds (4 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Very high strain energy (32.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-29.853
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
33
heavy atoms
MW
488
Da
LogP
5.52
cLogP
Final rank
4.4121
rank score
Inter norm
-1.002
normalised
Contacts
23
H-bonds 8
Strain ΔE
32.8 kcal/mol
SASA buried
81%
Lipo contact
83% BSA apolar/total
SASA unbound
749 Ų
Apolar buried
508 Ų

Interaction summary

HBA 4 HY 4 PI 1 CLASH 8

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 overlap17Native recall0.81
Jaccard0.63RMSD-
HB strict6Strict recall0.40
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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
398 3.765973798591196 -0.997636 -31.4521 5 23 0 0.00 0.00 - no Open
437 4.412114066828967 -1.00151 -29.8533 8 23 17 0.81 0.36 - no Current
418 6.336929737625268 -0.868344 -21.7276 8 18 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 -29.853kcal/mol
Ligand efficiency (LE) -0.9046kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.976
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 488.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.52
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 70.36kcal/mol
Minimised FF energy 37.61kcal/mol

SASA & burial

✓ computed
SASA (unbound) 748.7Ų
Total solvent-accessible surface area of free ligand
BSA total 609.7Ų
Buried surface area upon binding
BSA apolar 507.9Ų
Hydrophobic contacts buried
BSA polar 101.8Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1511.3Ų
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 503.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)