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
14.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.82, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.409 kcal/mol/HA)
✓ Good fit quality (FQ -12.02)
✓ Strong H-bond network (15 bonds)
✓ Deep burial (74% SASA buried)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-29.587
kcal/mol
LE
-1.409
kcal/mol/HA
Fit Quality
-12.02
FQ (Leeson)
HAC
21
heavy atoms
MW
336
Da
LogP
3.17
cLogP
Interaction summary
HB 15
HY 5
PI 4
CLASH 2
⚠ Exposure 50%
Interaction summary
HB 15
HY 5
PI 4
CLASH 2
⚠ Exposure 50%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 6
Exposed 6
LogP 3.17
H-bonds 15
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 3.059 | Score | -29.587 |
|---|---|---|---|
| Inter norm | -1.412 | Intra norm | 0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 15 |
| Artifact reason | geometry warning; 5 clashes; 2 protein clashes | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
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 | 0.82 | 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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.587kcal/mol
Ligand efficiency (LE)
-1.4089kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.018
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
336.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.71kcal/mol
Minimised FF energy
15.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
558.2Ų
Total solvent-accessible surface area of free ligand
BSA total
415.8Ų
Buried surface area upon binding
BSA apolar
210.7Ų
Hydrophobic contacts buried
BSA polar
205.2Ų
Polar contacts buried
Fraction buried
74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
50.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2008.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
787.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)