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 high
Native strong
SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.29
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.155 kcal/mol/HA)
✓ Good fit quality (FQ -9.85)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (19.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.254
kcal/mol
LE
-1.155
kcal/mol/HA
Fit Quality
-9.85
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
2.45
cLogP
Final rank
1.7125
rank score
Inter norm
-1.303
normalised
Contacts
19
H-bonds 8
Interaction summary
HBD 1
HBA 5
PC 1
HY 5
PI 2
CLASH 2
Interaction summary
HBD 1
HBA 5
PC 1
HY 5
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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: permissive.
| 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 | 15 | Native recall | 0.79 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 2 | HB role recall | 0.29 |
| HB same residue | 3 | HB residue recall | 0.43 |
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
-24.254kcal/mol
Ligand efficiency (LE)
-1.1550kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.851
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.47kcal/mol
Minimised FF energy
-1.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
541.6Ų
Total solvent-accessible surface area of free ligand
BSA total
467.1Ų
Buried surface area upon binding
BSA apolar
331.6Ų
Hydrophobic contacts buried
BSA polar
135.5Ų
Polar contacts buried
Fraction buried
86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2494.9Ų
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
1371.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)