Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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
10.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.54, H-bond role recall 0.29
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.424 kcal/mol/HA)
✓ Good fit quality (FQ -12.37)
✓ Good H-bonds (3 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (10.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-31.334
kcal/mol
LE
-1.424
kcal/mol/HA
Fit Quality
-12.37
FQ (Leeson)
HAC
22
heavy atoms
MW
292
Da
LogP
3.93
cLogP
Final rank
2.8660
rank score
Inter norm
-1.331
normalised
Contacts
21
H-bonds 9
Interaction summary
HBD 1
HBA 2
PC 1
HY 4
PI 2
CLASH 4
Interaction summary
HBD 1
HBA 2
PC 1
HY 4
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 2 | Strict recall | 0.22 |
| HB same residue+role | 2 | HB role recall | 0.29 |
| HB same residue | 2 | HB residue recall | 0.29 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.334kcal/mol
Ligand efficiency (LE)
-1.4243kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.365
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
292.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.93
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.69kcal/mol
Minimised FF energy
43.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
542.6Ų
Total solvent-accessible surface area of free ligand
BSA total
486.4Ų
Buried surface area upon binding
BSA apolar
413.7Ų
Hydrophobic contacts buried
BSA polar
72.7Ų
Polar contacts buried
Fraction buried
89.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2558.0Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1373.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)