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
23.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.56
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (15/25 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.819 kcal/mol/HA)
✓ Good fit quality (FQ -8.05)
✓ Strong H-bond network (16 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (23.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-26.209
kcal/mol
LE
-0.819
kcal/mol/HA
Fit Quality
-8.05
FQ (Leeson)
HAC
32
heavy atoms
MW
438
Da
LogP
4.28
cLogP
Interaction summary
HB 16
HY 8
PI 3
CLASH 4
⚠ Exposure 60%
Interaction summary
HB 16
HY 8
PI 3
CLASH 4
⚠ Exposure 60%
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (15/25 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 25
Buried (contacted) 10
Exposed 15
LogP 4.28
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.235 | Score | -26.209 |
|---|---|---|---|
| Inter norm | -0.940 | Intra norm | 0.121 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 16 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 23.6 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
MET75
PRO12
SER71
TYR46
| ||
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 | ||
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 | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 6 | HB residue recall | 0.75 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 260 | 1.1082347513979987 | -0.775134 | -20.4397 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 2.4599060132209662 | -0.840741 | -20.296 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 289 | 2.81667322176217 | -0.671287 | -17.9163 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 289 | 3.2353618255927503 | -0.939527 | -26.2086 | 16 | 15 | 13 | 0.93 | 0.56 | - | no | Current |
| 237 | 3.4895145128219167 | -1.02523 | -24.5452 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 3.5497150933488077 | -0.655457 | -19.1227 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 4.017419003236659 | -0.919734 | -21.9628 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 5.7079837755049425 | -0.760916 | -19.7213 | 10 | 14 | 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
-26.209kcal/mol
Ligand efficiency (LE)
-0.8190kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.054
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.28
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.80kcal/mol
Minimised FF energy
25.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
721.7Ų
Total solvent-accessible surface area of free ligand
BSA total
436.1Ų
Buried surface area upon binding
BSA apolar
328.1Ų
Hydrophobic contacts buried
BSA polar
108.1Ų
Polar contacts buried
Fraction buried
60.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2309.3Ų
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
762.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)