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
7.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.5 kcal/mol)
✓ Excellent LE (-1.252 kcal/mol/HA)
✓ Good fit quality (FQ -11.05)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-28.785
kcal/mol
LE
-1.252
kcal/mol/HA
Fit Quality
-11.05
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.89
cLogP
Interaction summary
HB 12
HY 6
PI 2
CLASH 1
⚠ Exposure 56%
Interaction summary
HB 12
HY 6
PI 2
CLASH 1
⚠ Exposure 56%
Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 7
Exposed 9
LogP 1.89
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.472 | Score | -28.785 |
|---|---|---|---|
| Inter norm | -1.327 | Intra norm | 0.075 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ALA102
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
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 | 0.79 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 554 | 0.2203022561644955 | -1.36019 | -30.3993 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 1.6542963930149828 | -1.18885 | -26.8787 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 573 | 2.71578287337706 | -1.10311 | -22.1924 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 570 | 3.0587130104782503 | -1.48918 | -33.393 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 3.4718491156602886 | -1.32651 | -28.7854 | 12 | 18 | 15 | 0.94 | 0.50 | - | no | Current |
| 546 | 3.504691433720093 | -1.20709 | -25.4384 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 3.9343705953567754 | -1.06026 | -20.2148 | 13 | 16 | 5 | 0.31 | 0.20 | - | no | Open |
| 582 | 4.168655656750893 | -1.04725 | -22.6406 | 14 | 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
-28.785kcal/mol
Ligand efficiency (LE)
-1.2515kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.046
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
352.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-66.80kcal/mol
Minimised FF energy
-74.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
610.6Ų
Total solvent-accessible surface area of free ligand
BSA total
459.1Ų
Buried surface area upon binding
BSA apolar
334.4Ų
Hydrophobic contacts buried
BSA polar
124.8Ų
Polar contacts buried
Fraction buried
75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2114.5Ų
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
826.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)