Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
46.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.89
Reason: strain 46.4 kcal/mol
strain ΔE 46.4 kcal/mol
2 protein-contact clashes
59% of hydrophobic surface appears solvent-exposed (16/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.874 kcal/mol/HA)
✓ Good fit quality (FQ -8.88)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (46.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-31.463
kcal/mol
LE
-0.874
kcal/mol/HA
Fit Quality
-8.88
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
4.53
cLogP
Interaction summary
HB 13
HY 4
PI 2
CLASH 2
⚠ Exposure 59%
Interaction summary
HB 13
HY 4
PI 2
CLASH 2
⚠ Exposure 59%
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 (16/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 11
Exposed 16
LogP 4.53
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.270 | Score | -31.463 |
|---|---|---|---|
| Inter norm | -0.837 | Intra norm | -0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 13 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 46.4 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
MET75
PRO12
SER71
TYR46
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 9 | Strict recall | 0.75 |
| HB same residue+role | 8 | HB role recall | 0.89 |
| HB same residue | 7 | HB residue recall | 0.88 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 633 | 1.4534645373380197 | -0.793879 | -27.516 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 2.3901037565977243 | -0.85542 | -26.1748 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 4.27025805099335 | -0.83732 | -31.4633 | 13 | 18 | 13 | 0.93 | 0.89 | - | no | Current |
| 631 | 4.719625321008581 | -0.786061 | -29.5404 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 92 | 4.968528210764631 | -0.725531 | -27.5939 | 14 | 17 | 13 | 0.93 | 0.89 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.463kcal/mol
Ligand efficiency (LE)
-0.8740kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.883
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.53
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
162.89kcal/mol
Minimised FF energy
116.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
717.2Ų
Total solvent-accessible surface area of free ligand
BSA total
515.1Ų
Buried surface area upon binding
BSA apolar
359.7Ų
Hydrophobic contacts buried
BSA polar
155.4Ų
Polar contacts buried
Fraction buried
71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2263.7Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
760.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)