FAIRMol

KB_chagas_97

Pose ID 14345 Compound 4000 Pose 107

DB SELECTIONDocking 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 KB_chagas_97

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
13.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.72, H-bond role recall 0.45
Burial
91%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes 48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.217 kcal/mol/HA) ✓ Good fit quality (FQ -11.49) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (13.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-34.069
kcal/mol
LE
-1.217
kcal/mol/HA
Fit Quality
-11.49
FQ (Leeson)
HAC
28
heavy atoms
MW
412
Da
LogP
3.53
cLogP
Final rank
4.6365
rank score
Inter norm
-1.237
normalised
Contacts
22
H-bonds 11
Strain ΔE
13.7 kcal/mol
SASA buried
91%
Lipo contact
74% BSA apolar/total
SASA unbound
655 Ų
Apolar buried
442 Ų

Interaction summary

HBD 3 HBA 5 HY 3 PI 1 CLASH 2

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 overlap18Native recall0.86
Jaccard0.72RMSD-
HB strict7Strict recall0.47
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
172 1.9134998045254397 -0.79303 -20.8753 6 16 0 0.00 0.00 - no Open
181 2.8366532868781027 -0.68708 -18.3087 7 12 0 0.00 0.00 - no Open
107 2.9160797128979166 -0.986747 -26.1895 9 22 0 0.00 0.00 - no Open
126 4.1586623052380025 -0.847622 -21.9701 4 15 0 0.00 0.00 - no Open
107 4.636484064309373 -1.23657 -34.0694 11 22 18 0.86 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 -34.069kcal/mol
Ligand efficiency (LE) -1.2168kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.487
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 411.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.53
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 65.19kcal/mol
Minimised FF energy 51.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.4Ų
Total solvent-accessible surface area of free ligand
BSA total 595.6Ų
Buried surface area upon binding
BSA apolar 441.9Ų
Hydrophobic contacts buried
BSA polar 153.7Ų
Polar contacts buried
Fraction buried 90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1358.6Ų
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 509.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)