FAIRMol

Z57300836

Pose ID 14758 Compound 2814 Pose 520

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 Z57300836

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
14.5 kcal/mol
Protein clashes
13
Internal clashes
13
Native overlap
contact recall 0.57, Jaccard 0.44, H-bond role recall 0.36
Burial
81%
Hydrophobic fit
84%
Reason: 13 protein-contact clashes, 13 internal clashes
13 protein-contact clashes 13 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.084 kcal/mol/HA) ✓ Good fit quality (FQ -9.98) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (14.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.175
kcal/mol
LE
-1.084
kcal/mol/HA
Fit Quality
-9.98
FQ (Leeson)
HAC
26
heavy atoms
MW
387
Da
LogP
4.27
cLogP
Final rank
4.6230
rank score
Inter norm
-1.221
normalised
Contacts
18
H-bonds 10
Strain ΔE
14.5 kcal/mol
SASA buried
81%
Lipo contact
84% BSA apolar/total
SASA unbound
599 Ų
Apolar buried
407 Ų

Interaction summary

HBD 1 HBA 5 HY 3 PI 0 CLASH 13

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 overlap12Native recall0.57
Jaccard0.44RMSD-
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
492 1.118683972416749 -1.25558 -30.7347 3 14 0 0.00 0.00 - no Open
520 4.622975414032014 -1.22106 -28.1752 10 18 12 0.57 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 -28.175kcal/mol
Ligand efficiency (LE) -1.0837kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.984
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 386.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.27
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 4.88kcal/mol
Minimised FF energy -9.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 598.8Ų
Total solvent-accessible surface area of free ligand
BSA total 485.3Ų
Buried surface area upon binding
BSA apolar 407.1Ų
Hydrophobic contacts buried
BSA polar 78.2Ų
Polar contacts buried
Fraction buried 81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1352.7Ų
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 510.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)