FAIRMol

TC488

Pose ID 14453 Compound 1436 Pose 215

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 TC488

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 medium Native strong SASA done
Strain ΔE
32.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.95, H-bond role recall 0.36
Burial
72%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
1 protein-contact clashes 47% of hydrophobic surface appears solvent-exposed (14/30 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 (-0.784 kcal/mol/HA) ✓ Good fit quality (FQ -8.09) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (32.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-29.808
kcal/mol
LE
-0.784
kcal/mol/HA
Fit Quality
-8.09
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Strain ΔE
32.2 kcal/mol
SASA buried
72%
Lipo contact
84% BSA apolar/total
SASA unbound
845 Ų
Apolar buried
509 Ų

Interaction summary

HB 11 HY 14 PI 1 CLASH 1 ⚠ Exposure 46%

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
⚠️Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (14/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30 Buried (contacted) 16 Exposed 14 LogP 5.18 H-bonds 11
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank4.596Score-29.808
Inter norm-0.890Intra norm0.106
Top1000noExcludedno
Contacts22H-bonds11
Artifact reasongeometry warning; 15 clashes; 3 protein clashes; high strain Δ 32.2
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44

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 overlap21Native recall1.00
Jaccard0.95RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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
290 4.097676844008653 -0.78523 -28.0312 5 20 0 0.00 0.00 - no Open
215 4.595874156107308 -0.890462 -29.8082 11 22 21 1.00 0.36 - no Current
176 5.855540308270551 -0.790924 -25.3763 12 21 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 -29.808kcal/mol
Ligand efficiency (LE) -0.7844kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.087
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.18
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 134.35kcal/mol
Minimised FF energy 102.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 845.0Ų
Total solvent-accessible surface area of free ligand
BSA total 609.7Ų
Buried surface area upon binding
BSA apolar 509.2Ų
Hydrophobic contacts buried
BSA polar 100.5Ų
Polar contacts buried
Fraction buried 72.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1563.3Ų
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 530.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)