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
37.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.83, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
52% of hydrophobic surface appears solvent-exposed (12/23 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 (-0.827 kcal/mol/HA)
✓ Good fit quality (FQ -8.21)
✓ Good H-bonds (4 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (37.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-27.303
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-8.21
FQ (Leeson)
HAC
33
heavy atoms
MW
486
Da
LogP
4.13
cLogP
Final rank
3.5035
rank score
Inter norm
-1.011
normalised
Contacts
21
H-bonds 4
Interaction summary
HBA 4
HY 3
PI 1
CLASH 1
Interaction summary
HBA 4
HY 3
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 19 | Native recall | 0.90 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 484 | 1.6830606252738989 | -0.743187 | -19.2115 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 1.9789215848404698 | -0.917724 | -24.5812 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 2.5136273279812995 | -0.919656 | -24.9115 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 110 | 2.8793248649702754 | -0.805397 | -25.4557 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 126 | 2.9672521965662164 | -0.835595 | -16.7586 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 3.304468521208352 | -0.813519 | -25.9782 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 3.503518404096005 | -1.01121 | -27.3035 | 4 | 21 | 19 | 0.90 | 0.27 | - | no | Current |
| 473 | 3.7845323780093345 | -0.749603 | -15.8986 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 484 | 4.235486935676271 | -1.01852 | -28.93 | 6 | 19 | 19 | 0.90 | 0.36 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.303kcal/mol
Ligand efficiency (LE)
-0.8274kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.209
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.62kcal/mol
Minimised FF energy
30.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
777.4Ų
Total solvent-accessible surface area of free ligand
BSA total
584.6Ų
Buried surface area upon binding
BSA apolar
419.4Ų
Hydrophobic contacts buried
BSA polar
165.3Ų
Polar contacts buried
Fraction buried
75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1437.7Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
533.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)