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
14.7 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.44
Reason: 13 internal clashes
13 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (14/23 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
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
Yes
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.892 kcal/mol/HA)
✓ Good fit quality (FQ -8.60)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-26.750
kcal/mol
LE
-0.892
kcal/mol/HA
Fit Quality
-8.60
FQ (Leeson)
HAC
30
heavy atoms
MW
413
Da
LogP
5.30
cLogP
Final rank
4.2774
rank score
Inter norm
-0.922
normalised
Contacts
14
H-bonds 11
Interaction summary
HBA 7
HY 2
PI 3
CLASH 0
Interaction summary
HBA 7
HY 2
PI 3
CLASH 0
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
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: 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 | 12 | Native recall | 0.86 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 4 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 575 | 1.0399056885554303 | -0.751969 | -21.6104 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 1.2383004177190995 | -0.879713 | -24.9612 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 593 | 1.840988622981869 | -0.872435 | -23.9498 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 2.3276582312652585 | -0.752765 | -24.4998 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.6007481059821833 | -0.753229 | -21.5097 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 2.7382383736726044 | -1.03726 | -27.9313 | 6 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 594 | 3.260885981020757 | -0.879028 | -23.4199 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 3.268899464166515 | -1.08062 | -31.5572 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 605 | 4.277421972823018 | -0.921936 | -26.7502 | 11 | 14 | 12 | 0.86 | 0.44 | - | no | Current |
| 587 | 4.87930352531888 | -1.00805 | -27.8762 | 7 | 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
-26.750kcal/mol
Ligand efficiency (LE)
-0.8917kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.601
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
413.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.30
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.84kcal/mol
Minimised FF energy
45.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.5Ų
Total solvent-accessible surface area of free ligand
BSA total
435.4Ų
Buried surface area upon binding
BSA apolar
296.7Ų
Hydrophobic contacts buried
BSA polar
138.7Ų
Polar contacts buried
Fraction buried
65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2184.6Ų
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
789.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)