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
14.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.79, H-bond role recall 0.43
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.380 kcal/mol/HA)
✓ Good fit quality (FQ -11.06)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (14.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.834
kcal/mol
LE
-1.380
kcal/mol/HA
Fit Quality
-11.06
FQ (Leeson)
HAC
18
heavy atoms
MW
240
Da
LogP
2.50
cLogP
Interaction summary
HB 6
HY 5
PI 3
CLASH 3
Interaction summary
HB 6
HY 5
PI 3
CLASH 3
| Final rank | 1.774 | Score | -24.834 |
|---|---|---|---|
| Inter norm | -1.544 | Intra norm | 0.164 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ALA67
ARG154
ARG277
ASP88
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR389
| ||
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 | ||
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 4 | HB residue recall | 0.57 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 278 | -0.8574207073241159 | -1.70687 | -28.9721 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 1.5959075923798347 | -1.34226 | -22.3319 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 1.7738857891499675 | -1.54371 | -24.8335 | 6 | 15 | 15 | 0.79 | 0.43 | - | no | Current |
| 318 | 3.068718716092686 | -1.39908 | -21.0296 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 3.2507870146011015 | -1.76408 | -29.0198 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.834kcal/mol
Ligand efficiency (LE)
-1.3796kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.057
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
240.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.50
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.48kcal/mol
Minimised FF energy
22.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
447.0Ų
Total solvent-accessible surface area of free ligand
BSA total
390.1Ų
Buried surface area upon binding
BSA apolar
315.0Ų
Hydrophobic contacts buried
BSA polar
75.1Ų
Polar contacts buried
Fraction buried
87.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2444.9Ų
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
1382.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)