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
19.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.89, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.095 kcal/mol/HA)
✓ Good fit quality (FQ -9.67)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.193
kcal/mol
LE
-1.095
kcal/mol/HA
Fit Quality
-9.67
FQ (Leeson)
HAC
23
heavy atoms
MW
314
Da
LogP
1.19
cLogP
Interaction summary
HB 10
HY 10
PI 2
CLASH 1
⚠ Exposure 41%
Interaction summary
HB 10
HY 10
PI 2
CLASH 1
⚠ Exposure 41%
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
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP 1.19
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.096 | Score | -25.193 |
|---|---|---|---|
| Inter norm | -1.325 | Intra norm | 0.230 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 4 protein clashes | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
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 | 16 | Native recall | 1.00 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 628 | 0.18702354902015306 | -1.17891 | -22.6406 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 0.6285692150163996 | -1.03442 | -15.6318 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.579057013340084 | -1.22393 | -23.9439 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 2.6212597648646407 | -1.27144 | -23.7154 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 2.628679045735035 | -1.08796 | -19.974 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 2.942909683415412 | -1.07862 | -18.8879 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 4.096418414128663 | -1.32544 | -25.1928 | 10 | 18 | 16 | 1.00 | 0.40 | - | no | Current |
| 622 | 4.311340728481773 | -1.06258 | -19.8805 | 8 | 12 | 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
-25.193kcal/mol
Ligand efficiency (LE)
-1.0953kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.667
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
314.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.13kcal/mol
Minimised FF energy
28.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
603.8Ų
Total solvent-accessible surface area of free ligand
BSA total
456.1Ų
Buried surface area upon binding
BSA apolar
338.3Ų
Hydrophobic contacts buried
BSA polar
117.8Ų
Polar contacts buried
Fraction buried
75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2155.5Ų
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
782.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)