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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.88, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.800 kcal/mol/HA)
✓ Good fit quality (FQ -7.47)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (34.1 kcal/mol)
✗ Geometry warnings
Score
-21.614
kcal/mol
LE
-0.800
kcal/mol/HA
Fit Quality
-7.47
FQ (Leeson)
HAC
27
heavy atoms
MW
407
Da
LogP
-0.86
cLogP
Interaction summary
HB 11
HY 5
PI 0
CLASH 1
⚠ Exposure 44%
Interaction summary
HB 11
HY 5
PI 0
CLASH 1
⚠ Exposure 44%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 10
Exposed 8
LogP -0.86
H-bonds 11
Exposed fragments:
aliphatic chain/group (8 atoms exposed)
| Final rank | 2.491 | Score | -21.614 |
|---|---|---|---|
| Inter norm | -0.909 | Intra norm | 0.109 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 11 |
| Artifact reason | geometry warning; 4 clashes; 2 protein clashes; high strain Δ 34.1 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 14 | Native recall | 1.00 |
| Jaccard | 0.88 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 627 | 2.4905462346490186 | -0.909128 | -21.6145 | 11 | 16 | 14 | 1.00 | 0.67 | - | no | Current |
| 601 | 2.577096648107939 | -1.10395 | -26.3968 | 13 | 13 | 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
-21.614kcal/mol
Ligand efficiency (LE)
-0.8005kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.469
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
406.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.86
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
154.12kcal/mol
Minimised FF energy
120.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
653.6Ų
Total solvent-accessible surface area of free ligand
BSA total
498.8Ų
Buried surface area upon binding
BSA apolar
344.7Ų
Hydrophobic contacts buried
BSA polar
154.0Ų
Polar contacts buried
Fraction buried
76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2241.6Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
739.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)