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
18.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.83, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.854 kcal/mol/HA)
✓ Good fit quality (FQ -7.65)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (18.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-20.484
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-7.65
FQ (Leeson)
HAC
24
heavy atoms
MW
348
Da
LogP
1.24
cLogP
Interaction summary
HB 10
HY 5
PI 2
CLASH 1
⚠ Exposure 58%
Interaction summary
HB 10
HY 5
PI 2
CLASH 1
⚠ Exposure 58%
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
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 7
Exposed 10
LogP 1.24
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.766 | Score | -20.484 |
|---|---|---|---|
| Inter norm | -1.128 | Intra norm | 0.274 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 6 clashes; 4 protein clashes | ||
| Residues |
ALA102
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
CYS72
GLY73
GLY75
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 5 | HB residue recall | 0.50 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 563 | 1.8928814771868634 | -1.35453 | -27.4463 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.872704971680777 | -0.996415 | -15.7931 | 13 | 17 | 5 | 0.31 | 0.30 | - | no | Open |
| 592 | 3.431950118215558 | -0.961984 | -15.4549 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 586 | 4.280581100652397 | -1.48063 | -29.2583 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 570 | 4.765644166236609 | -1.12764 | -20.4843 | 10 | 17 | 15 | 0.94 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.484kcal/mol
Ligand efficiency (LE)
-0.8535kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.649
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-48.74kcal/mol
Minimised FF energy
-66.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
636.1Ų
Total solvent-accessible surface area of free ligand
BSA total
456.4Ų
Buried surface area upon binding
BSA apolar
329.1Ų
Hydrophobic contacts buried
BSA polar
127.3Ų
Polar contacts buried
Fraction buried
71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2152.0Ų
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
793.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)