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
31.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.63, H-bond role recall 0.67
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (14/20 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
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 (-0.915 kcal/mol/HA)
✓ Good fit quality (FQ -8.91)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Very high strain energy (31.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-28.355
kcal/mol
LE
-0.915
kcal/mol/HA
Fit Quality
-8.91
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
0.91
cLogP
Final rank
3.7391
rank score
Inter norm
-0.929
normalised
Contacts
17
H-bonds 14
Interaction summary
HBD 3
HBA 5
HY 2
PI 2
CLASH 3
Interaction summary
HBD 3
HBA 5
HY 2
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.
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 | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 12 | Native recall | 0.86 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 6 | HB residue recall | 0.75 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 653 | 2.722098138210943 | -0.699326 | -17.7051 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 2.950615041156466 | -0.809494 | -22.4875 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 629 | 3.204630439018359 | -0.928268 | -27.106 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 653 | 3.7390617616469473 | -0.929142 | -28.3549 | 14 | 17 | 12 | 0.86 | 0.67 | - | no | Current |
| 662 | 4.499574721337301 | -1.20282 | -33.9202 | 16 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 4.5950468675443386 | -0.839344 | -15.0638 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 4.7851696497644545 | -0.712218 | -21.0542 | 6 | 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
-28.355kcal/mol
Ligand efficiency (LE)
-0.9147kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.911
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.91
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.50kcal/mol
Minimised FF energy
37.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
688.6Ų
Total solvent-accessible surface area of free ligand
BSA total
513.2Ų
Buried surface area upon binding
BSA apolar
326.8Ų
Hydrophobic contacts buried
BSA polar
186.4Ų
Polar contacts buried
Fraction buried
74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2215.7Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
745.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)