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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
31.3 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.50
Reason: 8 internal clashes
8 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.855 kcal/mol/HA)
✓ Good fit quality (FQ -8.07)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-23.944
kcal/mol
LE
-0.855
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
3.56
cLogP
Final rank
2.8820
rank score
Inter norm
-1.000
normalised
Contacts
18
H-bonds 9
Interaction summary
HBD 1
HBA 5
HY 4
PI 4
CLASH 0
Interaction summary
HBD 1
HBA 5
HY 4
PI 4
CLASH 0
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
No clash · clashes detected for this pose.
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 400 | 1.4147632879637646 | -1.24423 | -31.4622 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 489 | 1.4638681084293472 | -0.961388 | -23.9647 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 431 | 2.4136684293931885 | -0.96178 | -24.5137 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 2.8819750065791108 | -0.999965 | -23.9442 | 9 | 18 | 14 | 0.88 | 0.50 | - | no | Current |
| 445 | 2.9258322476020324 | -0.918609 | -19.8413 | 8 | 17 | 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
-23.944kcal/mol
Ligand efficiency (LE)
-0.8551kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.073
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.27kcal/mol
Minimised FF energy
-14.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.9Ų
Total solvent-accessible surface area of free ligand
BSA total
481.5Ų
Buried surface area upon binding
BSA apolar
315.1Ų
Hydrophobic contacts buried
BSA polar
166.5Ų
Polar contacts buried
Fraction buried
73.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2173.9Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
765.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)