FAIRMol

Z443419884

Pose ID 14794 Compound 4062 Pose 556

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 Z443419884

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
25.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.55
Burial
91%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.045 kcal/mol/HA) ✓ Good fit quality (FQ -10.08) ✓ Good H-bonds (4 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (25.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-31.345
kcal/mol
LE
-1.045
kcal/mol/HA
Fit Quality
-10.08
FQ (Leeson)
HAC
30
heavy atoms
MW
483
Da
LogP
3.99
cLogP
Final rank
2.1081
rank score
Inter norm
-1.051
normalised
Contacts
21
H-bonds 8
Strain ΔE
25.6 kcal/mol
SASA buried
91%
Lipo contact
75% BSA apolar/total
SASA unbound
695 Ų
Apolar buried
472 Ų

Interaction summary

HBA 4 HY 4 PI 1 CLASH 1

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

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
Jaccard0.68RMSD-
HB strict7Strict recall0.47
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

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
556 2.1081321163138544 -1.051 -31.3445 8 21 17 0.81 0.55 - no Current
547 4.831100007018329 -0.966268 -27.5059 10 23 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 -31.345kcal/mol
Ligand efficiency (LE) -1.0448kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.079
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 483.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.99
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 199.54kcal/mol
Minimised FF energy 173.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 694.9Ų
Total solvent-accessible surface area of free ligand
BSA total 632.4Ų
Buried surface area upon binding
BSA apolar 471.9Ų
Hydrophobic contacts buried
BSA polar 160.6Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1398.1Ų
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 499.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)