FAIRMol

Z19455379

Pose ID 14638 Compound 2584 Pose 400

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 Z19455379

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 medium Native strong SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.45
Burial
86%
Hydrophobic fit
57%
Reason: no major geometry red flags detected
4 intramolecular clashes 40% of hydrophobic surface appears solvent-exposed (6/15 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 (-1.118 kcal/mol/HA) ✓ Good fit quality (FQ -10.02) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (86% SASA buried) ✗ Moderate strain (15.9 kcal/mol) ✗ Geometry warnings
Score
-26.839
kcal/mol
LE
-1.118
kcal/mol/HA
Fit Quality
-10.02
FQ (Leeson)
HAC
24
heavy atoms
MW
344
Da
LogP
1.88
cLogP
Strain ΔE
15.9 kcal/mol
SASA buried
86%
Lipo contact
57% BSA apolar/total
SASA unbound
584 Ų
Apolar buried
284 Ų

Interaction summary

HB 11 HY 9 PI 1 CLASH 0 ⚠ Exposure 40%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15 Buried (contacted) 9 Exposed 6 LogP 1.88 H-bonds 11
Exposed fragments: aliphatic chain/group (6 atoms exposed)
Final rank3.274Score-26.839
Inter norm-1.302Intra norm0.184
Top1000noExcludedno
Contacts18H-bonds11
Artifact reasongeometry warning; 4 clashes; 3 protein clashes
Residues
ALA24 ALA40 ASN41 GLN42 GLU43 GLU73 GLY23 GLY25 GLY71 LEU130 LEU39 LYS127 LYS26 PHE38 SER27 SER28 THR44 THR69

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 overlap14Native recall0.67
Jaccard0.56RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
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
386 1.839433879338239 -1.01234 -20.2213 5 18 0 0.00 0.00 - no Open
378 2.854415706722772 -1.19654 -26.2923 15 14 0 0.00 0.00 - no Open
400 3.2741913472875535 -1.30243 -26.8389 11 18 14 0.67 0.45 - 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 -26.839kcal/mol
Ligand efficiency (LE) -1.1183kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.022
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.88
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.33kcal/mol
Minimised FF energy 44.42kcal/mol

SASA & burial

✓ computed
SASA (unbound) 584.1Ų
Total solvent-accessible surface area of free ligand
BSA total 499.6Ų
Buried surface area upon binding
BSA apolar 283.9Ų
Hydrophobic contacts buried
BSA polar 215.7Ų
Polar contacts buried
Fraction buried 85.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1200.3Ų
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 509.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)