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 medium
Native strong
SASA done
Strain ΔE
15.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.60
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.893 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.015
kcal/mol
LE
-0.893
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
28
heavy atoms
MW
419
Da
LogP
3.01
cLogP
Interaction summary
HB 13
HY 7
PI 4
CLASH 5
⚠ Exposure 38%
Interaction summary
HB 13
HY 7
PI 4
CLASH 5
⚠ Exposure 38%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 11
Exposed 7
LogP 3.01
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)
| Final rank | 2.970 | Score | -25.015 |
|---|---|---|---|
| Inter norm | -1.088 | Intra norm | 0.194 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 13 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
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
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.88 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 7 | HB residue recall | 0.70 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 391 | 0.8112587710984578 | -0.883156 | -21.7804 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.761457712336876 | -1.18388 | -28.0949 | 12 | 17 | 16 | 1.00 | 0.70 | - | no | Open |
| 484 | 2.388298171391906 | -0.868572 | -20.6754 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 2.911216982679596 | -0.879119 | -20.3872 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 2.970006987126121 | -1.08769 | -25.015 | 13 | 16 | 15 | 0.94 | 0.60 | - | no | Current |
| 379 | 3.450130273935065 | -0.998633 | -22.0405 | 14 | 15 | 5 | 0.31 | 0.20 | - | no | Open |
| 423 | 3.7405836219795368 | -1.00578 | -24.1953 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 160 | 3.885655564123343 | -0.784425 | -18.1914 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 4.225272845749715 | -1.07342 | -27.2468 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 5.143261743022093 | -1.07475 | -24.8662 | 12 | 15 | 5 | 0.31 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.015kcal/mol
Ligand efficiency (LE)
-0.8934kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.434
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-27.64kcal/mol
Minimised FF energy
-43.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
669.2Ų
Total solvent-accessible surface area of free ligand
BSA total
493.9Ų
Buried surface area upon binding
BSA apolar
328.9Ų
Hydrophobic contacts buried
BSA polar
165.1Ų
Polar contacts buried
Fraction buried
73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2138.6Ų
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
770.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)