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 high
Native strong
SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.56
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.835 kcal/mol/HA)
✓ Good fit quality (FQ -7.88)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.378
kcal/mol
LE
-0.835
kcal/mol/HA
Fit Quality
-7.88
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
3.31
cLogP
Final rank
3.8696
rank score
Inter norm
-0.950
normalised
Contacts
16
H-bonds 10
Interaction summary
HBD 1
HBA 5
HY 3
PI 3
CLASH 2
Interaction summary
HBD 1
HBA 5
HY 3
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 0.76 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 552 | 1.4674467189468063 | -0.951939 | -21.2275 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 551 | 2.058397956551504 | -1.26163 | -35.075 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 2.5265455231135476 | -1.2438 | -41.7041 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 576 | 3.869636448834477 | -0.950247 | -23.3779 | 10 | 16 | 13 | 0.93 | 0.56 | - | no | Current |
| 565 | 3.9192596699025195 | -1.30875 | -32.8613 | 14 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 546 | 4.121821341473989 | -1.11086 | -28.1942 | 10 | 18 | 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
-23.378kcal/mol
Ligand efficiency (LE)
-0.8349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.882
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.31
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
116.38kcal/mol
Minimised FF energy
99.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.7Ų
Total solvent-accessible surface area of free ligand
BSA total
466.2Ų
Buried surface area upon binding
BSA apolar
369.8Ų
Hydrophobic contacts buried
BSA polar
96.5Ų
Polar contacts buried
Fraction buried
74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2201.9Ų
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
772.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)