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
18.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact 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
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.323 kcal/mol/HA)
✓ Good fit quality (FQ -12.34)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-35.712
kcal/mol
LE
-1.323
kcal/mol/HA
Fit Quality
-12.34
FQ (Leeson)
HAC
27
heavy atoms
MW
381
Da
LogP
1.83
cLogP
Final rank
5.1536
rank score
Inter norm
-1.227
normalised
Contacts
16
H-bonds 13
Interaction summary
HBA 9
HY 3
PI 4
CLASH 2
Interaction summary
HBA 9
HY 3
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 16 | Native recall | 1.00 |
| Jaccard | 1.00 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 662 | 2.387234550870066 | -0.875978 | -25.1448 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 2.7504368620559965 | -1.1322 | -31.8335 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 2.9348303597234553 | -1.04997 | -30.5922 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 3.054569518894309 | -1.19774 | -32.9591 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 3.994413850524842 | -0.746194 | -21.7975 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 5.153622008531141 | -1.22703 | -35.7123 | 13 | 16 | 16 | 1.00 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-35.712kcal/mol
Ligand efficiency (LE)
-1.3227kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.340
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
381.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.83
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.81kcal/mol
Minimised FF energy
43.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
623.1Ų
Total solvent-accessible surface area of free ligand
BSA total
436.3Ų
Buried surface area upon binding
BSA apolar
273.1Ų
Hydrophobic contacts buried
BSA polar
163.2Ų
Polar contacts buried
Fraction buried
70.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2129.2Ų
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
777.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)