FAIRMol

TC410

Pose ID 14451 Compound 742 Pose 213

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 TC410

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
16.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.95, Jaccard 0.80, H-bond role recall 0.45
Burial
89%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 44% of hydrophobic surface appears solvent-exposed (8/18 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 (-1.103 kcal/mol/HA) ✓ Good fit quality (FQ -10.16) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (16.9 kcal/mol) ✗ Geometry warnings
Score
-28.677
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-10.16
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.45
cLogP
Final rank
2.9638
rank score
Inter norm
-1.241
normalised
Contacts
24
H-bonds 16
Strain ΔE
16.9 kcal/mol
SASA buried
89%
Lipo contact
86% BSA apolar/total
SASA unbound
637 Ų
Apolar buried
491 Ų

Interaction summary

HBA 7 HY 3 PI 1 CLASH 5

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 overlap20Native recall0.95
Jaccard0.80RMSD-
HB strict8Strict recall0.53
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
232 0.22512664578509115 -0.982056 -23.3495 2 18 0 0.00 0.00 - no Open
203 0.6142823023382752 -1.00213 -23.6948 7 19 0 0.00 0.00 - no Open
285 1.1222800013457437 -0.984396 -22.608 4 16 0 0.00 0.00 - no Open
238 1.9179388927226144 -1.20382 -29.2649 8 16 0 0.00 0.00 - no Open
234 2.1949120016563737 -1.18622 -28.0822 8 16 0 0.00 0.00 - no Open
341 2.442548170009624 -0.972273 -22.0173 8 14 0 0.00 0.00 - no Open
213 2.9637696841486436 -1.24057 -28.6769 16 24 20 0.95 0.45 - no Current
167 3.258232707517787 -1.05416 -24.6519 12 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 -28.677kcal/mol
Ligand efficiency (LE) -1.1030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.162
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.45
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 42.71kcal/mol
Minimised FF energy 25.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 637.0Ų
Total solvent-accessible surface area of free ligand
BSA total 568.2Ų
Buried surface area upon binding
BSA apolar 490.8Ų
Hydrophobic contacts buried
BSA polar 77.4Ų
Polar contacts buried
Fraction buried 89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1420.0Ų
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 503.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)