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 high
Native strong
SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (7/16 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. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -7.63)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-19.328
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-7.63
FQ (Leeson)
HAC
22
heavy atoms
MW
299
Da
LogP
2.74
cLogP
Final rank
3.1881
rank score
Inter norm
-1.128
normalised
Contacts
15
H-bonds 10
Interaction summary
HBD 2
HBA 5
HY 3
PI 3
CLASH 1
Interaction summary
HBD 2
HBA 5
HY 3
PI 3
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 221 | -0.5342035848569257 | -1.48191 | -28.3703 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 1.589293489537325 | -1.07316 | -17.7732 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 168 | 1.7994056093051762 | -1.25927 | -24.9338 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 156 | 2.1823482137671677 | -1.33711 | -18.3838 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 244 | 2.632384898312331 | -1.30724 | -22.0766 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 3.05553725405528 | -1.31477 | -25.7881 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 3.1880861317190305 | -1.12817 | -19.3279 | 10 | 15 | 13 | 0.93 | 0.67 | - | no | Current |
| 155 | 4.489595302255546 | -1.27909 | -22.1697 | 11 | 18 | 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
-19.328kcal/mol
Ligand efficiency (LE)
-0.8785kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.627
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
299.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.74
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.97kcal/mol
Minimised FF energy
26.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
545.9Ų
Total solvent-accessible surface area of free ligand
BSA total
389.2Ų
Buried surface area upon binding
BSA apolar
287.1Ų
Hydrophobic contacts buried
BSA polar
102.2Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2112.9Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
810.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)