FAIRMol

Z45612920

Pose ID 14771 Compound 3713 Pose 533

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 Z45612920

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.7 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.36
Burial
78%
Hydrophobic fit
80%
Reason: 1 severe internal clashes, 9 protein-contact clashes, 9 internal clashes
1 severe internal clashes 9 protein-contact clashes 9 intramolecular clashes 95% of hydrophobic surface is solvent-exposed (19/20 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 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 Medium Ames Clear DILI Risk
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.037 kcal/mol/HA) ✓ Good fit quality (FQ -9.79) ✓ Good H-bonds (5 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (11.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.029
kcal/mol
LE
-1.037
kcal/mol/HA
Fit Quality
-9.79
FQ (Leeson)
HAC
28
heavy atoms
MW
416
Da
LogP
5.35
cLogP
Final rank
4.9446
rank score
Inter norm
-1.077
normalised
Contacts
18
H-bonds 7
Strain ΔE
11.7 kcal/mol
SASA buried
78%
Lipo contact
80% BSA apolar/total
SASA unbound
657 Ų
Apolar buried
412 Ų

Interaction summary

HBA 5 HY 3 PI 0 CLASH 9 Severe 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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

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
Jaccard0.50RMSD-
HB strict5Strict recall0.33
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
516 0.4241926104561533 -1.1173 -26.1813 3 21 0 0.00 0.00 - no Open
541 2.5898260359995993 -0.875689 -22.4799 3 15 0 0.00 0.00 - no Open
533 4.94459793995519 -1.07721 -29.0291 7 18 13 0.62 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 -29.029kcal/mol
Ligand efficiency (LE) -1.0368kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.787
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.35
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 4.36kcal/mol
Minimised FF energy -7.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.8Ų
Total solvent-accessible surface area of free ligand
BSA total 515.6Ų
Buried surface area upon binding
BSA apolar 411.7Ų
Hydrophobic contacts buried
BSA polar 103.9Ų
Polar contacts buried
Fraction buried 78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1368.1Ų
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 541.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)