Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
26.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.36
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
76% of hydrophobic surface is solvent-exposed (22/29 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.649 kcal/mol/HA)
✓ Good fit quality (FQ -6.64)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-24.009
kcal/mol
LE
-0.649
kcal/mol/HA
Fit Quality
-6.64
FQ (Leeson)
HAC
37
heavy atoms
MW
501
Da
LogP
4.88
cLogP
Final rank
5.6978
rank score
Inter norm
-0.760
normalised
Contacts
18
H-bonds 14
Interaction summary
HBD 1
HBA 10
HY 2
PI 1
CLASH 3
Interaction summary
HBD 1
HBA 10
HY 2
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 17 | Native recall | 1.00 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 6 | HB residue recall | 0.55 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 294 | 1.245508240700725 | -0.728849 | -25.9836 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 1.930187225320806 | -0.655486 | -21.8232 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 3.2272343925835325 | -0.816086 | -23.0339 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 293 | 3.3208224858699698 | -0.781481 | -24.4604 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 290 | 3.749228973927113 | -0.629948 | -20.9201 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 194 | 3.909806676956081 | -0.745338 | -25.6544 | 8 | 15 | 4 | 0.24 | 0.18 | - | no | Open |
| 374 | 4.34931664373597 | -0.650967 | -19.125 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 179 | 5.697827032796828 | -0.75975 | -24.0093 | 14 | 18 | 17 | 1.00 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.009kcal/mol
Ligand efficiency (LE)
-0.6489kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.643
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
500.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.88
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.87kcal/mol
Minimised FF energy
94.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
776.1Ų
Total solvent-accessible surface area of free ligand
BSA total
514.6Ų
Buried surface area upon binding
BSA apolar
404.4Ų
Hydrophobic contacts buried
BSA polar
110.3Ų
Polar contacts buried
Fraction buried
66.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2372.9Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
693.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)