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
12.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.63, H-bond role recall 0.60
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 Low
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.119 kcal/mol/HA)
✓ Good fit quality (FQ -10.03)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (12.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-26.866
kcal/mol
LE
-1.119
kcal/mol/HA
Fit Quality
-10.03
FQ (Leeson)
HAC
24
heavy atoms
MW
354
Da
LogP
4.65
cLogP
Final rank
2.8543
rank score
Inter norm
-1.171
normalised
Contacts
15
H-bonds 9
Interaction summary
HBA 6
HY 5
PI 4
CLASH 4
Interaction summary
HBA 6
HY 5
PI 4
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 12 | Native recall | 0.75 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 6 | HB residue recall | 0.60 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | -0.18784752275886354 | -1.01592 | -23.8653 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 0.044810234807672045 | -1.09043 | -25.2406 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 0.05669390183562073 | -1.09591 | -25.194 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 0.2488068813182308 | -1.18196 | -27.8753 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 1.2946467321758754 | -1.18634 | -27.2383 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 2.0117884778778174 | -1.01577 | -22.8536 | 10 | 15 | 4 | 0.25 | 0.20 | - | no | Open |
| 372 | 2.25182953308986 | -1.35937 | -32.3799 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 2.8542622317418695 | -1.17081 | -26.8659 | 9 | 15 | 12 | 0.75 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.866kcal/mol
Ligand efficiency (LE)
-1.1194kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.032
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
354.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.65
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.84kcal/mol
Minimised FF energy
4.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.1Ų
Total solvent-accessible surface area of free ligand
BSA total
446.8Ų
Buried surface area upon binding
BSA apolar
292.4Ų
Hydrophobic contacts buried
BSA polar
154.4Ų
Polar contacts buried
Fraction buried
74.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2104.4Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
788.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)