FAIRMol

Z87656593

Pose ID 14649 Compound 3962 Pose 411

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 Z87656593

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 and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
17.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.95, Jaccard 0.87, H-bond role recall 0.45
Burial
87%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes 68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.237 kcal/mol/HA) ✓ Good fit quality (FQ -11.67) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Moderate strain (17.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-34.624
kcal/mol
LE
-1.237
kcal/mol/HA
Fit Quality
-11.67
FQ (Leeson)
HAC
28
heavy atoms
MW
422
Da
LogP
2.13
cLogP
Final rank
4.0948
rank score
Inter norm
-1.308
normalised
Contacts
22
H-bonds 10
Strain ΔE
17.8 kcal/mol
SASA buried
87%
Lipo contact
70% BSA apolar/total
SASA unbound
678 Ų
Apolar buried
412 Ų

Interaction summary

HBD 1 HBA 6 HY 3 PI 1 CLASH 1

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 overlap20Native recall0.95
Jaccard0.87RMSD-
HB strict7Strict recall0.47
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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
411 4.094844457063474 -1.30783 -34.6245 10 22 20 0.95 0.45 - no Current
393 6.771266076426603 -0.963748 -27.4884 13 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 -34.624kcal/mol
Ligand efficiency (LE) -1.2366kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.674
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 421.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.13
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -107.92kcal/mol
Minimised FF energy -125.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 677.6Ų
Total solvent-accessible surface area of free ligand
BSA total 588.4Ų
Buried surface area upon binding
BSA apolar 412.0Ų
Hydrophobic contacts buried
BSA polar 176.3Ų
Polar contacts buried
Fraction buried 86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1353.3Ų
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 497.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)