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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
26.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.57, H-bond role recall 0.43
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.875 kcal/mol/HA)
✓ Good fit quality (FQ -8.35)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (26.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-25.363
kcal/mol
LE
-0.875
kcal/mol/HA
Fit Quality
-8.35
FQ (Leeson)
HAC
29
heavy atoms
MW
404
Da
LogP
4.67
cLogP
Interaction summary
HB 7
HY 23
PI 5
CLASH 1
Interaction summary
HB 7
HY 23
PI 5
CLASH 1
| Final rank | 2.707 | Score | -25.363 |
|---|---|---|---|
| Inter norm | -1.021 | Intra norm | 0.146 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 7 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; moderate strain Δ 26.0 | ||
| Residues |
ALA67
ARG277
ASN327
ASP332
CYS328
GLU274
GLY236
GLY237
GLY276
GLY393
HIS197
LYS69
PRO275
SER200
TYR331
TYR389
VAL392
| ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 494 | 1.1577042796268664 | -0.806499 | -20.9573 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 452 | 1.5916735758417686 | -1.10999 | -27.3548 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 1.697784199305133 | -0.945349 | -17.4477 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 1.9753143606479693 | -0.828598 | -16.278 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 2.7071296605498025 | -1.02096 | -25.3626 | 7 | 17 | 13 | 0.68 | 0.43 | - | no | Current |
| 463 | 3.0485298790569324 | -0.939335 | -24.8709 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 3.9486253783950946 | -1.03556 | -23.1969 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 4.0865649410255696 | -0.835591 | -19.7943 | 5 | 12 | 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
-25.363kcal/mol
Ligand efficiency (LE)
-0.8746kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.348
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
404.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.39kcal/mol
Minimised FF energy
40.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
668.5Ų
Total solvent-accessible surface area of free ligand
BSA total
486.5Ų
Buried surface area upon binding
BSA apolar
389.9Ų
Hydrophobic contacts buried
BSA polar
96.6Ų
Polar contacts buried
Fraction buried
72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2592.4Ų
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
1417.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)