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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
12.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.93, Jaccard 0.72, H-bond role recall 0.89
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (10/16 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.984 kcal/mol/HA)
✓ Good fit quality (FQ -8.69)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (12.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-22.641
kcal/mol
LE
-0.984
kcal/mol/HA
Fit Quality
-8.69
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.89
cLogP
Interaction summary
HB 14
HY 4
PI 2
CLASH 4
⚠ Exposure 62%
Interaction summary
HB 14
HY 4
PI 2
CLASH 4
⚠ Exposure 62%
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
62% of hydrophobic surface is solvent-exposed (10/16 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 16
Buried (contacted) 6
Exposed 10
LogP 1.89
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.169 | Score | -22.641 |
|---|---|---|---|
| Inter norm | -1.047 | Intra norm | 0.063 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
MET98
SER99
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 | 0.72 | RMSD | - |
| HB strict | 10 | Strict recall | 0.83 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 554 | 0.2203022561644955 | -1.36019 | -30.3993 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 1.6542963930149828 | -1.18885 | -26.8787 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 573 | 2.71578287337706 | -1.10311 | -22.1924 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 570 | 3.0587130104782503 | -1.48918 | -33.393 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 3.4718491156602886 | -1.32651 | -28.7854 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 546 | 3.504691433720093 | -1.20709 | -25.4384 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 3.9343705953567754 | -1.06026 | -20.2148 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.168655656750893 | -1.04725 | -22.6406 | 14 | 17 | 13 | 0.93 | 0.89 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.641kcal/mol
Ligand efficiency (LE)
-0.9844kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.688
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
352.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-62.21kcal/mol
Minimised FF energy
-74.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
610.6Ų
Total solvent-accessible surface area of free ligand
BSA total
418.8Ų
Buried surface area upon binding
BSA apolar
292.5Ų
Hydrophobic contacts buried
BSA polar
126.2Ų
Polar contacts buried
Fraction buried
68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2152.7Ų
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
813.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)