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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
33.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.56
Reason: no major geometry red flags detected
1 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.010 kcal/mol/HA)
✓ Good fit quality (FQ -9.05)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (33.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (10)
Score
-24.234
kcal/mol
LE
-1.010
kcal/mol/HA
Fit Quality
-9.05
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
4.56
cLogP
Interaction summary
HB 7
HY 5
PI 2
CLASH 1
⚠ Exposure 64%
Interaction summary
HB 7
HY 5
PI 2
CLASH 1
⚠ Exposure 64%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 6
Exposed 11
LogP 4.56
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 1.062 | Score | -24.234 |
|---|---|---|---|
| Inter norm | -1.146 | Intra norm | 0.136 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 10 clashes; 6 protein contact clashes; high strain Δ 33.7 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER43
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 | 0.81 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 6 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 437 | 1.0622373773057405 | -1.14598 | -24.2338 | 7 | 15 | 13 | 0.93 | 0.56 | - | no | Current |
| 384 | 1.6543390194869305 | -1.30146 | -32.1781 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 1.8894308683503533 | -1.45598 | -31.2552 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 2.420917382962812 | -1.29827 | -28.0042 | 14 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 2.9718852536009854 | -0.815124 | -17.3361 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 421 | 4.01819321477796 | -0.930807 | -22.6703 | 10 | 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
-24.234kcal/mol
Ligand efficiency (LE)
-1.0097kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.049
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.73kcal/mol
Minimised FF energy
75.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.9Ų
Total solvent-accessible surface area of free ligand
BSA total
437.1Ų
Buried surface area upon binding
BSA apolar
344.6Ų
Hydrophobic contacts buried
BSA polar
92.5Ų
Polar contacts buried
Fraction buried
69.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2178.1Ų
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
802.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)